Dataset Error Report

[Vignesh291]

Hi I received the error while trying to create a database (mspurity)

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/computational- metabolomics/mspurity_createdatabase/mspurity_createdatabase/1.16.2+galaxy1.

Details Execution resulted in the following messages:

Fatal error: Exit code 1 ()

Tool generated the following standard error:

Loading required package: Rcpp Warning messages: 1: package ‘msPurity’ was built under R version 4.0.3 2: package ‘Rcpp’ was built under R version 4.0.3 Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel Loading required package: MSnbase Loading required package: mzR Loading required package: S4Vectors Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

smooth

This is MSnbase version 2.16.0 Visit https://lgatto.github.io/MSnbase/ to get started.

Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

trimws

This is xcms version 3.12.0

Attaching package: ‘xcms’

The following object is masked from ‘package:stats’:

sigma

Warning messages: 1: package ‘xcms’ was built under R version 4.0.3 2: package ‘Biobase’ was built under R version 4.0.3 3: package ‘BiocParallel’ was built under R version 4.0.3 4: package ‘MSnbase’ was built under R version 4.0.3 5: package ‘mzR’ was built under R version 4.0.3 6: package ‘S4Vectors’ was built under R version 4.0.3 7: package ‘ProtGenerics’ was built under R version 4.0.3 Warning message: package ‘CAMERA’ was built under R version 4.0.3 Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. Creating a database of fragmentation spectra and LC features Error in $<-.data.frame(*tmp*, "grp_name", value = c("M451T96", "M451T1042", : replacement has 426 rows, data has 696 Calls: <Anonymous> -> export2sqlite -> $<- -> $<-.data.frame Execution halted

[jorainer]

Are you sure this is an error related to xcms? I don't see which function from xcms was actually called to result in this error...

[Vignesh291]

I have an error related to xcms in another work flow. Can you clarify it??

WhenI use xcmsfindchrompeaks xcmsset, I get the following note in the Tool Standard Error:

"you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis."

SESSION INFO R version 4.0.3 (2020-10-10) Main packages: 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 RColorBrewer 1.1.2 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

image /shared/ifbstor1/galaxy/datasets/004/226/dataset_4226601.dat BPPARAM 2 method CentWave ppm 5 peakwidth c(4, 20) snthresh 10 prefilter c(3, 100) mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 0 verboseColumns FALSE peaklist FALSE

ARGUMENTS PROCESSING INFO


INFILE PROCESSING INFO


MAIN PROCESSING INFO
	COMPUTE
		Apply filter[s] (if asked)
		Chromatographic peak detection

Object of class: CentWaveParam Parameters: ppm: 5 peakwidth: 4, 20 snthresh: 10 prefilter: 3, 100 mzCenterFun: wMean integrate: 1 mzdiff: -0.001 fitgauss: FALSE noise: 0 verboseColumns: FALSE roiList length: 0 firstBaselineCheck TRUE roiScales length: 0 Creating the sampleMetadata file...

WARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names() In your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files: fraction 1 -> fraction.1 Error in R_nc4_open: NetCDF: Unknown file format

XCMSnExp OBJECT INFO

MSn experiment data ("XCMSnExp") Object size in memory: 1.39 Mb

• • • Spectra data - - - MS level(s): 1 Number of spectra: 4016 MSn retention times: 0:56 - 27:2 minutes
• • • Processing information - - - Data loaded [Thu Feb 2 09:23:43 2023] Filter: select MS level(s) 1. [Thu Feb 2 09:25:07 2023] MSnbase version: 2.16.1
• • • Meta data - - - phenoData rowNames: fraction 1.mzXML varLabels: sample_name sample_group varMetadata: labelDescription Loaded from: fraction 1.mzXML protocolData: none featureData featureNames: F1.S0001 F1.S0002 ... F1.S4680 (4016 total) fvarLabels: fileIdx spIdx ... spectrum (35 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)'
• • • xcms preprocessing - - - Chromatographic peak detection: method: centWave 667 peaks identified in 1 samples. On average 667 chromatographic peaks per sample.

    xcmsSet OBJECT INFO An "xcmsSet" object with 1 samples

Time range: 68.9-1620.2 seconds (1.1-27 minutes) Mass range: 452.3575-1347.4827 m/z Peaks: 667 (about 667 per sample) Peak Groups: 0 Sample classes: .

Feature detection: o Peak picking performed on MS1. o Scan range limited to 1 - 4680 Profile settings: method = bin step = 0.1

Memory usage: 0.724 MB

DONE

[jorainer]

where do you get this output from? this does not look like typical output from R. Also, the message you see is not an error but a warning (you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.). what that means is that you converted the newer XCMSnExp data class into the old (deprecated) xcmsSet and that during that conversion the variable "sampclass" that was used in xcmsSet to define the class labels from an analysis was not set (as it is no longer supported).

[sneumann]

This seems to come from Workflow4Metabolomics (ifbstor1/galaxy/datasets), and if this is not an issue with the parameters, we'll have to work with the W4M people ( e.g. @fgiacomoni) on fixing their wrappers or something in xcms. The 3.12.0 is a bit dated. Is that the newest version installed ? Yours, Steffen

[Vignesh291]

I am new to working with XCMS in galaxy. I am not sure if that was the newest version installed. I will recheck my sample metadata and try running the workflow again. Thanks for your comments.