When I used xcms plot chromatogram on the Rdata file obtained after fillPeaks or after group (the 2nd step of group after retcor), I got the following error :
Execution resulted in the following messages:
- Fatal error: Exit code 1 ()*
Tool generated the following standard error: - Error in .mz_chromatograms(object, mz = "mz") : *
- Chromatograms in row 1 have different mz*
- Calls: chromatogram ... featureDefinitions -> .local -> mz -> mz -> .local -> .mz_chromatograms*
Execution halted
Then, I used xcms plot chromatogram on the Rdata file obtained after retcor : it's ok, I was able to have the BPI and the TIC so it's not necessary for me to have the BPI and the TIC after this step (but I guess it's important to report errors encountered).
I can send you the beginning of the tool standard output but not the whole because the project on which I am working is confidential...
*SESSION INFO R version 4.0.3 (2020-10-10) Main packages: RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 Other loaded packages: SummarizedExperiment 1.20.0 lattice 0.20.41 colorspace 2.0.0 vctrs 0.3.7 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.10 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.12 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.3 tools 4.0.3 bitops 1.0.6 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.53.1 ellipsis 0.3.1 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.3 *
ARGUMENTS INFO images /shared/ifbstor1/galaxy/datasets/001/573/dataset_1573842.dat sampleMetadata /shared/ifbstor1/galaxy/datasets/001/559/dataset_1559269.dat