Open Vignesh291 opened 1 year ago
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...
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
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
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).
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
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.
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’:
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Welcome to Bioconductor
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’:
Loading required package: ProtGenerics
Attaching package: ‘ProtGenerics’
The following object is masked from ‘package:stats’:
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’:
This is xcms version 3.12.0
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
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 -> export2sqlite -> $<- -> $<-.data.frame
Execution halted
$<-.data.frame
(*tmp*
, "grp_name", value = c("M451T96", "M451T1042", : replacement has 426 rows, data has 696 Calls: