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annotate runit/output/information.txt @ 2:3f8ae071bdda draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author ethevenot
date Mon, 22 Jan 2018 11:32:41 -0500
parents 4753e64cf694
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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1
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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2 Start of the 'proFIA' Galaxy module call: Mon 08 Jan 2018 07:23:11 PM
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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3 files_root_directory plasFIA
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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5 1) Peak detection step ('proFIAset'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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7 2) Peak alignment ('group.FIA'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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9 707 groups have been done .
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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11 3) Creating the peak table ('makeDataMatrix'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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13 4) Imputing missing values ('impute.randomForest'):
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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14 missForest iteration 1 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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15 missForest iteration 2 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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16 missForest iteration 3 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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17 missForest iteration 4 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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18 missForest iteration 5 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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19 missForest iteration 6 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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20 missForest iteration 7 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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21 missForest iteration 8 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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22 missForest iteration 9 in progress...done!
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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23 missForest iteration 10 in progress...done!
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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25 5) Plotting ('plot'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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26 PCA
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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27 3 samples x 707 variables
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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28 standard scaling of predictors
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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29 R2X(cum) pre ort
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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30 Total 1 2 0
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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31 null device
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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32 1
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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34 6) Printing ('show'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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35 A "proFIAset" object containing 1 classes.
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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36 Data matrix has been created.
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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37 2089 peaks detected.
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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38 707 features have been grouped.
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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39 The data matrix is avalaible.
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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40 Memory usage: 0.409 MB
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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42 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
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43
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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44 End of 'proFIA' Galaxy module call: 2018-01-08 19:27:06
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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48 ============================================================================
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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49 Additional information about the call:
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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51 1) Parameters:
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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52 value
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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53 dataMatrix_out "./output/dataMatrix.tsv"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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54 sampleMetadata_out "./output/sampleMetadata.tsv"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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55 variableMetadata_out "./output/variableMetadata.tsv"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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56 figure "./output/figure.pdf"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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57 information "./output/information.txt"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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58 zipfile "./plasfia/plasFIA.zip"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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59 library "NULL"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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60 ppmN "2"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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61 dmzN "5e-04"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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62 ppmGroupN "1"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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63 dmzGroupN "5e-04"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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64 fracGroupN "0.1"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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65 imputeC "randomForest"
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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66
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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67 2) Session Info:
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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68 R version 3.3.1 (2016-06-21)
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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69 Main packages:
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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70 proFIA 1.4.0 xcms 1.50.1 Biobase 2.34.0 ProtGenerics 1.6.0 BiocGenerics 0.20.0 mzR 2.8.1 Rcpp 0.12.10 batch 1.1.4
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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71 Other loaded packages:
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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72 splines 3.3.1 itertools 0.1.3 MASS 7.3.45 BiocParallel 1.8.1 missForest 1.4 lattice 0.20.34 quadprog 1.5.5 foreach 1.4.4 plyr 1.8.4 grid 3.3.1 iterators 1.0.9 multtest 2.30.0 survival 2.41.2 randomForest 4.6.12 Matrix 1.2.8 RColorBrewer 1.1.2 S4Vectors 0.12.2 codetools 0.2.15 MassSpecWavelet 1.40.0 pracma 1.9.9 ropls 1.6.2 stats4 3.3.1 minpack.lm 1.2.1 RANN 2.5
3f8ae071bdda planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 1
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73 ============================================================================