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comparison 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
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1:4753e64cf694 2:3f8ae071bdda
1 1
2 Start of the 'proFIA' Galaxy module call: Wed 03 May 2017 01:18:28 PM 2 Start of the 'proFIA' Galaxy module call: Mon 08 Jan 2018 07:23:11 PM
3 files_root_directory plasFIA 3 files_root_directory plasFIA
4 4
5 1) Peak detection step ('proFIAset'): 5 1) Peak detection step ('proFIAset'):
6 6
7 2) Peak alignment ('group.FIA'): 7 2) Peak alignment ('group.FIA'):
8 8
9 722 groups have been done . 9 707 groups have been done .
10 10
11 3) Creating the peak table ('makeDataMatrix'): 11 3) Creating the peak table ('makeDataMatrix'):
12 12
13 4) Imputing missing values ('imputeMissingValues.WKNN_TN'): 13 4) Imputing missing values ('impute.randomForest'):
14 missForest iteration 1 in progress...done!
15 missForest iteration 2 in progress...done!
16 missForest iteration 3 in progress...done!
17 missForest iteration 4 in progress...done!
18 missForest iteration 5 in progress...done!
19 missForest iteration 6 in progress...done!
20 missForest iteration 7 in progress...done!
21 missForest iteration 8 in progress...done!
22 missForest iteration 9 in progress...done!
23 missForest iteration 10 in progress...done!
14 24
15 5) Plotting ('plot'): 25 5) Plotting ('plot'):
16 PCA 26 PCA
17 3 samples x 644 variables 27 3 samples x 707 variables
18 standard scaling of predictors 28 standard scaling of predictors
19 78 excluded variables (near zero variance)
20 R2X(cum) pre ort 29 R2X(cum) pre ort
21 Total 1 2 0 30 Total 1 2 0
22 null device 31 null device
23 1 32 1
24 33
25 6) Printing ('show'): 34 6) Printing ('show'):
26 A "proFIAset" object containing 1 classes. 35 A "proFIAset" object containing 1 classes.
27 Missing values have been imputed. 36 Data matrix has been created.
28 2101 peaks detected. 37 2089 peaks detected.
29 722 features have been grouped. 38 707 features have been grouped.
30 The data matrix is avalaible. 39 The data matrix is avalaible.
31 Memory usage: 0.419 MB 40 Memory usage: 0.409 MB
32 41
33 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'): 42 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):
34 43
35 End of 'proFIA' Galaxy module call: 2017-05-03 13:27:09 44 End of 'proFIA' Galaxy module call: 2018-01-08 19:27:06
45
46
47
48 ============================================================================
49 Additional information about the call:
50
51 1) Parameters:
52 value
53 dataMatrix_out "./output/dataMatrix.tsv"
54 sampleMetadata_out "./output/sampleMetadata.tsv"
55 variableMetadata_out "./output/variableMetadata.tsv"
56 figure "./output/figure.pdf"
57 information "./output/information.txt"
58 zipfile "./plasfia/plasFIA.zip"
59 library "NULL"
60 ppmN "2"
61 dmzN "5e-04"
62 ppmGroupN "1"
63 dmzGroupN "5e-04"
64 fracGroupN "0.1"
65 imputeC "randomForest"
66
67 2) Session Info:
68 R version 3.3.1 (2016-06-21)
69 Main packages:
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
71 Other loaded packages:
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
73 ============================================================================