Mercurial > repos > ethevenot > profia
comparison runit/output/information.txt @ 2:3f8ae071bdda draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author | ethevenot |
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date | Mon, 22 Jan 2018 11:32:41 -0500 |
parents | 4753e64cf694 |
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1:4753e64cf694 | 2:3f8ae071bdda |
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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 ============================================================================ |