Mercurial > repos > ethevenot > profia
view 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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Start of the 'proFIA' Galaxy module call: Mon 08 Jan 2018 07:23:11 PM files_root_directory plasFIA 1) Peak detection step ('proFIAset'): 2) Peak alignment ('group.FIA'): 707 groups have been done . 3) Creating the peak table ('makeDataMatrix'): 4) Imputing missing values ('impute.randomForest'): missForest iteration 1 in progress...done! missForest iteration 2 in progress...done! missForest iteration 3 in progress...done! missForest iteration 4 in progress...done! missForest iteration 5 in progress...done! missForest iteration 6 in progress...done! missForest iteration 7 in progress...done! missForest iteration 8 in progress...done! missForest iteration 9 in progress...done! missForest iteration 10 in progress...done! 5) Plotting ('plot'): PCA 3 samples x 707 variables standard scaling of predictors R2X(cum) pre ort Total 1 2 0 null device 1 6) Printing ('show'): A "proFIAset" object containing 1 classes. Data matrix has been created. 2089 peaks detected. 707 features have been grouped. The data matrix is avalaible. Memory usage: 0.409 MB 7) Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'): End of 'proFIA' Galaxy module call: 2018-01-08 19:27:06 ============================================================================ Additional information about the call: 1) Parameters: value dataMatrix_out "./output/dataMatrix.tsv" sampleMetadata_out "./output/sampleMetadata.tsv" variableMetadata_out "./output/variableMetadata.tsv" figure "./output/figure.pdf" information "./output/information.txt" zipfile "./plasfia/plasFIA.zip" library "NULL" ppmN "2" dmzN "5e-04" ppmGroupN "1" dmzGroupN "5e-04" fracGroupN "0.1" imputeC "randomForest" 2) Session Info: R version 3.3.1 (2016-06-21) Main packages: 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 Other loaded packages: 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 ============================================================================