Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2 #984

gxydevbot · 2025-10-08T00:19:33Z

Hello! This is an automated update of the following workflow: workflows/metabolomics/lcms-preprocessing. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.3.0 should be updated to toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/2.0.1

The workflow release number has been updated from 1.1 to 1.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

github-actions · 2025-10-08T00:45:56Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: SampleMetadata:
- step_state: scheduled
Step 2: Mass-spectrometry Dataset Collection:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/3820e3f3b1cb/xcms_group/xcms_group.r image '/tmp/tmp16fkh5mz/files/0/f/1/dataset_0f16453c-e9d9-474c-a3cf-053ff392e65a.dat'  method PeakDensity bw 5.0 minFraction 0.9 minSamples 1 binSize 0.01 maxFeatures 50   convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE       ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Processing 187837 mz slices ... OK
There were 50 or more warnings (use warnings() to see the first 50)
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/0/f/1/dataset_0f16453c-e9d9-474c-a3cf-053ff392e65a.dat
method	PeakDensity
bw	5
minFraction	0.9
minSamples	1
binSize	0.01
maxFeatures	50
convertRTMinute	FALSE
numDigitsMZ	4
numDigitsRT	0
intval	into
naTOzero	TRUE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Perform the correspondence
Object of class:  PeakDensityParam 
Parameters:
 sampleGroups: character of length 12 
 bw: 5 
 minFraction: 0.9 
 minSamples: 1 
 binSize: 0.01 
 maxFeatures: 50 
		DRAW GRAPHICS
null device 
          1 


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 6.43 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: -1:58 - 19:2 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 34716 peaks identified in 12 samples.
 On average 2893 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 
Correspondence:
 method: chromatographic peak density 
 2230 features identified.
 Median mz range of features: 0.00028742
 Median rt range of features: 1.6196


	xcmsSet OBJECT INFO
An "xcmsSet" object with 12 samples

Time range: 1.1-1141.8 seconds (0-19 minutes)
Mass range: 50.025-989.2024 m/z
Peaks: 34716 (about 2893 per sample)
Peak Groups: 2230 
Sample classes: blk, sample, QC 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 9.09 MB




	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
methods	`{"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.01", "bw": "5.0", "method": "PeakDensity", "minFraction": "0.9", "minSamples": "1"}`
peaklist	`{"__current_case__": 0, "convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"}`

Step 12: toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/2.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method_cond	`{"__current_case__": 1, "chosen_stat": ["NA"], "class_col": "class", "method": "each_class", "test_fold_cond": {"__current_case__": 1, "test_fold": "No"}}`

Step 13: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/a8d866a71ba1/xcms_fillpeaks/xcms_fillpeaks.r  image '/tmp/tmp16fkh5mz/files/9/8/e/dataset_98e15ad3-fa5e-4cc0-9635-b385d672b06a.dat'  expandMz 0 expandRt 0 ppm 0   convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE       ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Defining peak areas for filling-in .... OK
Start integrating peak areas from original files
Requesting 1955 peaks from Blanc05.mzML ... got 82.
Requesting 1942 peaks from Blanc10.mzML ... got 86.
Requesting 1927 peaks from Blanc16.mzML ... got 147.
Requesting 622 peaks from HU_neg_048.mzML ... got 316.
Requesting 509 peaks from HU_neg_090.mzML ... got 315.
Requesting 576 peaks from HU_neg_123.mzML ... got 342.
Requesting 514 peaks from HU_neg_157.mzML ... got 331.
Requesting 847 peaks from HU_neg_173.mzML ... got 426.
Requesting 510 peaks from HU_neg_192.mzML ... got 313.
Requesting 123 peaks from QC1_002.mzML ... got 103.
Requesting 110 peaks from QC1_008.mzML ... got 95.
Requesting 132 peaks from QC1_014.mzML ... got 111.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/9/8/e/dataset_98e15ad3-fa5e-4cc0-9635-b385d672b06a.dat
expandMz	0
expandRt	0
ppm	0
convertRTMinute	FALSE
numDigitsMZ	4
numDigitsRT	0
intval	into
naTOzero	TRUE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Filling missing peaks using default settings
Object of class:  FillChromPeaksParam 
Parameters:
 expandMz: 0 
 expandRt: 0 
 ppm: 0 


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 6.44 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: -1:58 - 19:2 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 37383 peaks identified in 12 samples.
 On average 3115 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 
Correspondence:
 method: chromatographic peak density 
 2230 features identified.
 Median mz range of features: 0.00028742
 Median rt range of features: 1.6196
 2667 filled peaks (on average 222.25 per sample).


	xcmsSet OBJECT INFO
An "xcmsSet" object with 12 samples

Time range: 1.1-1141.8 seconds (0-19 minutes)
Mass range: 50.025-989.2024 m/z
Peaks: 37383 (about 3115 per sample)
Peak Groups: 2230 
Sample classes: blk, sample, QC 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 9.53 MB




	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
Adv	`{"expandMz": "0", "expandRt": "0", "ppm": "0"}`
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
peaklist	`{"convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"}`

Step 14: toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.7+camera1.48.0-galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/75a1b3f7bacc/camera_annotate//CAMERA_annotateDiffreport.r image '/tmp/tmp16fkh5mz/files/e/3/a/dataset_e3abd6dd-b981-47e9-b2c8-bc8f7f0c618d.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 2 maxiso 4 minfrac 0.5  quick TRUE    convertRTMinute TRUE numDigitsMZ 4 numDigitsRT 2 intval into

Exit Code:

```
0
```

Standard Error:

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

Standard Output:

	SESSION INFO
R version 4.1.0 (2021-05-18) 
Main packages:
batch 1.1.5 	multtest 2.48.0 	CAMERA 1.48.0 	xcms 3.14.0 	MSnbase 2.18.0 	ProtGenerics 1.24.0 	S4Vectors 0.30.0 	mzR 2.26.0 	Rcpp 1.0.6 	BiocParallel 1.26.0 	Biobase 2.52.0 	BiocGenerics 0.38.0 	
Other loaded packages:
bitops 1.0.7 	matrixStats 0.59.0 	doParallel 1.0.16 	RColorBrewer 1.1.2 	GenomeInfoDb 1.28.0 	tools 4.1.0 	backports 1.2.1 	utf8 1.2.1 	R6 2.5.0 	affyio 1.62.0 	rpart 4.1.15 	Hmisc 4.5.0 	colorspace 2.0.2 	nnet 7.3.16 	gridExtra 2.3 	compiler 4.1.0 	MassSpecWavelet 1.58.0 	preprocessCore 1.54.0 	graph 1.70.0 	htmlTable 2.2.1 	DelayedArray 0.18.0 	scales 1.1.1 	checkmate 2.0.0 	DEoptimR 1.0.9 	robustbase 0.93.8 	affy 1.70.0 	RBGL 1.68.0 	stringr 1.4.0 	digest 0.6.27 	foreign 0.8.81 	XVector 0.32.0 	base64enc 0.1.3 	jpeg 0.1.8.1 	pkgconfig 2.0.3 	htmltools 0.5.1.1 	MatrixGenerics 1.4.0 	limma 3.48.0 	htmlwidgets 1.5.3 	rlang 0.4.11 	rstudioapi 0.13 	impute 1.66.0 	mzID 1.30.0 	RCurl 1.98.1.3 	magrittr 2.0.1 	GenomeInfoDbData 1.2.6 	Formula 1.2.4 	MALDIquant 1.19.3 	Matrix 1.3.4 	munsell 0.5.0 	fansi 0.4.2 	MsCoreUtils 1.4.0 	lifecycle 1.0.0 	vsn 3.60.0 	stringi 1.6.2 	MASS 7.3.54 	SummarizedExperiment 1.22.0 	zlibbioc 1.38.0 	plyr 1.8.6 	grid 4.1.0 	crayon 1.4.1 	lattice 0.20.44 	splines 4.1.0 	knitr 1.33 	pillar 1.6.1 	igraph 1.2.6 	GenomicRanges 1.44.0 	codetools 0.2.18 	XML 3.99.0.6 	glue 1.4.2 	latticeExtra 0.6.29 	data.table 1.14.0 	pcaMethods 1.84.0 	BiocManager 1.30.16 	vctrs 0.3.8 	png 0.1.7 	foreach 1.5.1 	gtable 0.3.0 	RANN 2.6.1 	clue 0.3.59 	ggplot2 3.3.5 	xfun 0.24 	ncdf4 1.17 	survival 3.2.11 	tibble 3.1.2 	iterators 1.0.13 	IRanges 2.26.0 	cluster 2.1.2 	ellipsis 0.3.2 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/e/3/a/dataset_e3abd6dd-b981-47e9-b2c8-bc8f7f0c618d.dat
nSlaves	1
sigma	6
perfwhm	0.6
ppm	5
mzabs	0.015
maxcharge	2
maxiso	4
minfrac	0.5
quick	TRUE
convertRTMinute	TRUE
numDigitsMZ	4
numDigitsRT	2
intval	into


	INFILE PROCESSING INFO


	ARGUMENTS PROCESSING INFO


	MAIN PROCESSING INFO
Start grouping after retention time.
Created 313 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
 % finished: 10  20  30  40  50  60  70  80  90  100  
Found isotopes: 304 
[1] "converting the retention times into minutes in the variableMetadata"


	XSET OBJECT INFO
An "xsAnnotate" object!
With 313 groups (pseudospectra)
With 12 samples and 2230 peaks
Polarity mode is set to:   
Using automatic sample selection
Annotated isotopes: 304 
Memory usage: 10.7 MB




	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"rdata.xcms.fillpeaks"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
diffreport	`{"options": {"__current_case__": 1, "option": "hide"}}`
export	`{"convertRTMinute": true, "intval": "into", "numDigitsMZ": "4", "numDigitsRT": "2"}`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
findgeneral	`{"mzabs": "0.015", "ppm": "5"}`
findisotopes	`{"maxcharge": "2", "maxiso": "4", "minfrac": "0.5"}`
groupfwhm	`{"perfwhm": "0.6", "sigma": "6"}`
quick_block	`{"__current_case__": 1, "polarity": "quick", "quick": "TRUE"}`

Step 3: toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/2/d/3/dataset_2d3fafad-83a2-449a-bc71-ee0a4b832acd.dat' singlefile_sampleName 'Blanc05.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/2/d/3/dataset_2d3fafad-83a2-449a-bc71-ee0a4b832acd.dat
singlefile_sampleName	Blanc05.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
Blanc05.mzML     Blanc05            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.77 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2022 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc05.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2022 (2022 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
Blanc05.mzML     Blanc05            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/b/1/e/dataset_b1ef1269-5a01-45c3-bc08-b80042337cd9.dat' singlefile_sampleName 'QC1_008.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/b/1/e/dataset_b1ef1269-5a01-45c3-bc08-b80042337cd9.dat
singlefile_sampleName	QC1_008.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
QC1_008.mzML     QC1_008            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.72 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1879 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_008.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_008.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1879 (1879 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
QC1_008.mzML     QC1_008            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 3:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/1/2/f/dataset_12ff9ef4-b7e8-471d-b9d0-5fe758db5164.dat' singlefile_sampleName 'QC1_002.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/1/2/f/dataset_12ff9ef4-b7e8-471d-b9d0-5fe758db5164.dat
singlefile_sampleName	QC1_002.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
QC1_002.mzML     QC1_002            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.78 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2039 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_002.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_002.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2039 (2039 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
QC1_002.mzML     QC1_002            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 4:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/5/9/f/dataset_59f819f2-f411-4a24-b595-8f6b2938998e.dat' singlefile_sampleName 'QC1_014.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/5/9/f/dataset_59f819f2-f411-4a24-b595-8f6b2938998e.dat
singlefile_sampleName	QC1_014.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
QC1_014.mzML     QC1_014            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.59 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1533 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_014.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_014.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1533 (1533 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
QC1_014.mzML     QC1_014            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 5:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/4/1/1/dataset_411b3baa-cf72-4d3f-a58e-567bf1065468.dat' singlefile_sampleName 'HU_neg_123.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/4/1/1/dataset_411b3baa-cf72-4d3f-a58e-567bf1065468.dat
singlefile_sampleName	HU_neg_123.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_123.mzML  HU_neg_123            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.72 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1892 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:16 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_123.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_123.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1892 (1892 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_123.mzML  HU_neg_123            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 6:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/e/6/3/dataset_e63cd723-ef8f-46d1-92d7-3c7993c83da1.dat' singlefile_sampleName 'HU_neg_192.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/e/6/3/dataset_e63cd723-ef8f-46d1-92d7-3c7993c83da1.dat
singlefile_sampleName	HU_neg_192.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_192.mzML  HU_neg_192            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1647 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:17 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_192.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_192.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1647 (1647 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_192.mzML  HU_neg_192            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 7:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/b/b/a/dataset_bba7a609-0ad2-4216-a520-2f1fd4ab5fb5.dat' singlefile_sampleName 'HU_neg_048.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/b/b/a/dataset_bba7a609-0ad2-4216-a520-2f1fd4ab5fb5.dat
singlefile_sampleName	HU_neg_048.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_048.mzML  HU_neg_048            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.77 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2031 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_048.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_048.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2031 (2031 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_048.mzML  HU_neg_048            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 8:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/8/1/e/dataset_81e7ae30-af1c-495d-9482-bef19a428be9.dat' singlefile_sampleName 'HU_neg_090.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/8/1/e/dataset_81e7ae30-af1c-495d-9482-bef19a428be9.dat
singlefile_sampleName	HU_neg_090.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_090.mzML  HU_neg_090            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.76 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1991 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_090.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_090.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1991 (1991 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_090.mzML  HU_neg_090            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 9:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/e/f/5/dataset_ef57c919-23c0-4201-a2c3-6e38fe2dfba4.dat' singlefile_sampleName 'HU_neg_157.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/e/f/5/dataset_ef57c919-23c0-4201-a2c3-6e38fe2dfba4.dat
singlefile_sampleName	HU_neg_157.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_157.mzML  HU_neg_157            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.68 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1767 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:16 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_157.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_157.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1767 (1767 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_157.mzML  HU_neg_157            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 10:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/7/3/1/dataset_731af266-4a13-43e3-a9d9-368cbd4ff159.dat' singlefile_sampleName 'HU_neg_173.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/7/3/1/dataset_731af266-4a13-43e3-a9d9-368cbd4ff159.dat
singlefile_sampleName	HU_neg_173.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
                sample_name sample_group
HU_neg_173.mzML  HU_neg_173            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.66 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1710 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:17 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_173.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_173.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1710 (1710 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
                sample_name sample_group
HU_neg_173.mzML  HU_neg_173            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 11:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/4/f/4/dataset_4f47538f-56f2-4d9c-b578-3c1dcc01c1c0.dat' singlefile_sampleName 'Blanc10.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/4/f/4/dataset_4f47538f-56f2-4d9c-b578-3c1dcc01c1c0.dat
singlefile_sampleName	Blanc10.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
Blanc10.mzML     Blanc10            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.72 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1882 
 MSn retention times: 0:1 - 18:59 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc10.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc10.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1882 (1882 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
Blanc10.mzML     Blanc10            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Job 12:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp16fkh5mz/files/f/3/6/dataset_f363beb3-7b91-456d-a798-0735506567a0.dat' singlefile_sampleName 'Blanc16.mzML'   ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	MSnbase 2.16.1 	ProtGenerics 1.22.0 	S4Vectors 0.28.1 	mzR 2.24.1 	Rcpp 1.0.6 	Biobase 2.50.0 	BiocGenerics 0.36.0 	
Other loaded packages:
pillar 1.6.0 	compiler 4.0.5 	BiocManager 1.30.15 	plyr 1.8.6 	iterators 1.0.13 	zlibbioc 1.36.0 	digest 0.6.27 	ncdf4 1.17 	MALDIquant 1.19.3 	lifecycle 1.0.0 	tibble 3.1.1 	preprocessCore 1.52.1 	gtable 0.3.0 	lattice 0.20.44 	pkgconfig 2.0.3 	rlang 0.4.11 	foreach 1.5.1 	IRanges 2.24.1 	vctrs 0.3.8 	grid 4.0.5 	glue 1.4.2 	impute 1.64.0 	R6 2.5.0 	fansi 0.4.2 	XML 3.99.0.6 	BiocParallel 1.24.1 	limma 3.46.0 	ggplot2 3.3.3 	magrittr 2.0.1 	scales 1.1.1 	pcaMethods 1.82.0 	codetools 0.2.18 	ellipsis 0.3.2 	MASS 7.3.54 	mzID 1.28.0 	colorspace 2.0.1 	utf8 1.2.1 	affy 1.68.0 	doParallel 1.0.16 	munsell 0.5.0 	vsn 3.58.0 	crayon 1.4.1 	affyio 1.60.0 	


	ARGUMENTS INFO
singlefile_galaxyPath	/tmp/tmp16fkh5mz/files/f/3/6/dataset_f363beb3-7b91-456d-a798-0735506567a0.dat
singlefile_sampleName	Blanc16.mzML


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
Blanc16.mzML     Blanc16            .
			Load Raw Data
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	MSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.57 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1485 
 MSn retention times: 0:1 - 18:59 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc16.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc16.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1485 (1485 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
Blanc16.mzML     Blanc16            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzml"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/9291271ec4d9/xcms_plot_chromatogram/xcms_plot_chromatogram.r  images 'c("/tmp/tmp16fkh5mz/files/a/f/5/dataset_af53d62e-5e99-4d0b-9b0e-c82e3a416ec9.dat","/tmp/tmp16fkh5mz/files/b/1/d/dataset_b1d1797c-c68d-401f-8e4f-4a95dae724c2.dat","/tmp/tmp16fkh5mz/files/2/c/7/dataset_2c79a9be-2c76-43ae-80a7-6ed769a871d3.dat","/tmp/tmp16fkh5mz/files/e/d/c/dataset_edccee4d-a8f3-455d-9731-2955defb72f8.dat","/tmp/tmp16fkh5mz/files/5/6/7/dataset_567023a4-6c30-4a88-a725-3f8e42e40bc8.dat","/tmp/tmp16fkh5mz/files/9/5/f/dataset_95f4718b-c9f1-4c6b-969f-fa9b6e73090f.dat","/tmp/tmp16fkh5mz/files/4/7/7/dataset_477b829d-2248-4f83-a49f-e529fd9a5eaf.dat","/tmp/tmp16fkh5mz/files/1/2/4/dataset_1242c172-ab70-4f13-a1b2-21f69056d0ce.dat","/tmp/tmp16fkh5mz/files/4/d/9/dataset_4d98e102-d02a-4344-9771-604112fe0329.dat","/tmp/tmp16fkh5mz/files/a/c/3/dataset_ac366934-5dbb-40e4-9c23-6f936871349d.dat","/tmp/tmp16fkh5mz/files/d/6/9/dataset_d6953858-7912-42f9-bc5f-37d872e4c1fb.dat","/tmp/tmp16fkh5mz/files/3/d/b/dataset_3dba5967-75b5-4518-bad4-1e989e55b62a.dat")'  sampleMetadata '/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat'

Exit Code:

```
0
```

Standard Error:

There were 12 warnings (use warnings() to see them)
There were 12 warnings (use warnings() to see them)

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
images	c("/tmp/tmp16fkh5mz/files/a/f/5/dataset_af53d62e-5e99-4d0b-9b0e-c82e3a416ec9.dat", "/tmp/tmp16fkh5mz/files/b/1/d/dataset_b1d1797c-c68d-401f-8e4f-4a95dae724c2.dat", "/tmp/tmp16fkh5mz/files/2/c/7/dataset_2c79a9be-2c76-43ae-80a7-6ed769a871d3.dat", "/tmp/tmp16fkh5mz/files/e/d/c/dataset_edccee4d-a8f3-455d-9731-2955defb72f8.dat", "/tmp/tmp16fkh5mz/files/5/6/7/dataset_567023a4-6c30-4a88-a725-3f8e42e40bc8.dat", "/tmp/tmp16fkh5mz/files/9/5/f/dataset_95f4718b-c9f1-4c6b-969f-fa9b6e73090f.dat", "/tmp/tmp16fkh5mz/files/4/7/7/dataset_477b829d-2248-4f83-a49f-e529fd9a5eaf.dat", 
"/tmp/tmp16fkh5mz/files/1/2/4/dataset_1242c172-ab70-4f13-a1b2-21f69056d0ce.dat", "/tmp/tmp16fkh5mz/files/4/d/9/dataset_4d98e102-d02a-4344-9771-604112fe0329.dat", "/tmp/tmp16fkh5mz/files/a/c/3/dataset_ac366934-5dbb-40e4-9c23-6f936871349d.dat", "/tmp/tmp16fkh5mz/files/d/6/9/dataset_d6953858-7912-42f9-bc5f-37d872e4c1fb.dat", "/tmp/tmp16fkh5mz/files/3/d/b/dataset_3dba5967-75b5-4518-bad4-1e989e55b62a.dat")
sampleMetadata	/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Blanc05 
Blanc10 
Blanc16 
HU_neg_048 
HU_neg_090 
HU_neg_123 
HU_neg_157 
HU_neg_173 
HU_neg_192 
QC1_002 
QC1_008 
QC1_014 
	XSET PHENODATA SETTING...


	MAIN PROCESSING INFO
		DRAW GRAPHICS
			Compute TIC
			Compute BPI
null device 
          1 
null device 
          1 


	XCMSnExp OBJECT INFO
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 6.23 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:27 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

Step 5: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/1/2/4/dataset_1242c172-ab70-4f13-a1b2-21f69056d0ce.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 5440 regions of interest ... OK: 3051 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/1/2/4/dataset_1242c172-ab70-4f13-a1b2-21f69056d0ce.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.67 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1710 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:17 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_173.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_173.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1710 (1710 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3051 peaks identified in 1 samples.
 On average 3051 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 4.4-1139.2 seconds (0.1-19 minutes)
Mass range: 50.0321-774.0387 m/z
Peaks: 3051 (about 3051 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1710 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.718 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 2:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/2/c/7/dataset_2c79a9be-2c76-43ae-80a7-6ed769a871d3.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 977 regions of interest ... OK: 848 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/2/c/7/dataset_2c79a9be-2c76-43ae-80a7-6ed769a871d3.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.58 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1485 
 MSn retention times: 0:1 - 18:59 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc16.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc16.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1485 (1485 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 848 peaks identified in 1 samples.
 On average 848 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 6.1-1138.6 seconds (0.1-19 minutes)
Mass range: 65.2841-963.0739 m/z
Peaks: 848 (about 848 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1485 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.364 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 3:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/e/d/c/dataset_edccee4d-a8f3-455d-9731-2955defb72f8.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 8869 regions of interest ... OK: 3343 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/e/d/c/dataset_edccee4d-a8f3-455d-9731-2955defb72f8.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.78 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2031 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_048.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_048.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2031 (2031 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3343 peaks identified in 1 samples.
 On average 3343 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 10.2-1139.3 seconds (0.2-19 minutes)
Mass range: 50.0321-988.5896 m/z
Peaks: 3343 (about 3343 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2031 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.809 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 4:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/5/6/7/dataset_567023a4-6c30-4a88-a725-3f8e42e40bc8.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 9690 regions of interest ... OK: 3868 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/5/6/7/dataset_567023a4-6c30-4a88-a725-3f8e42e40bc8.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.77 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1991 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_090.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_090.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1991 (1991 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3868 peaks identified in 1 samples.
 On average 3868 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 5.1-1139.5 seconds (0.1-19 minutes)
Mass range: 50.0321-987.5531 m/z
Peaks: 3868 (about 3868 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1991 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.879 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 5:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/d/6/9/dataset_d6953858-7912-42f9-bc5f-37d872e4c1fb.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 7872 regions of interest ... OK: 3881 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/d/6/9/dataset_d6953858-7912-42f9-bc5f-37d872e4c1fb.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.73 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1879 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_008.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_008.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1879 (1879 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3881 peaks identified in 1 samples.
 On average 3881 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 2-1139.3 seconds (0-19 minutes)
Mass range: 50.0321-987.0559 m/z
Peaks: 3881 (about 3881 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1879 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.864 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 6:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/3/d/b/dataset_3dba5967-75b5-4518-bad4-1e989e55b62a.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 5007 regions of interest ... OK: 3599 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/3/d/b/dataset_3dba5967-75b5-4518-bad4-1e989e55b62a.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.6 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1533 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:02 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_014.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_014.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1533 (1533 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3599 peaks identified in 1 samples.
 On average 3599 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 2.1-1138.8 seconds (0-19 minutes)
Mass range: 50.0321-963.0639 m/z
Peaks: 3599 (about 3599 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1533 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.77 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 7:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/a/c/3/dataset_ac366934-5dbb-40e4-9c23-6f936871349d.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 8700 regions of interest ... OK: 3327 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/a/c/3/dataset_ac366934-5dbb-40e4-9c23-6f936871349d.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.79 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2039 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: QC1_002.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  QC1_002.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2039 (2039 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3327 peaks identified in 1 samples.
 On average 3327 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 4-1139.1 seconds (0.1-19 minutes)
Mass range: 50.0321-963.0398 m/z
Peaks: 3327 (about 3327 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.808 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 8:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/b/1/d/dataset_b1d1797c-c68d-401f-8e4f-4a95dae724c2.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 4136 regions of interest ... OK: 770 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/b/1/d/dataset_b1d1797c-c68d-401f-8e4f-4a95dae724c2.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.73 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1882 
 MSn retention times: 0:1 - 18:59 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc10.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc10.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1882 (1882 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 770 peaks identified in 1 samples.
 On average 770 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 2.7-1139 seconds (0-19 minutes)
Mass range: 65.2842-963.063 m/z
Peaks: 770 (about 770 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1882 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.413 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 9:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/9/5/f/dataset_95f4718b-c9f1-4c6b-969f-fa9b6e73090f.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 7597 regions of interest ... OK: 3408 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/9/5/f/dataset_95f4718b-c9f1-4c6b-969f-fa9b6e73090f.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.73 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1892 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:16 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_123.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_123.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1892 (1892 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3408 peaks identified in 1 samples.
 On average 3408 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 6-1136 seconds (0.1-18.9 minutes)
Mass range: 50.0321-963.0516 m/z
Peaks: 3408 (about 3408 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1892 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.797 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 10:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/4/7/7/dataset_477b829d-2248-4f83-a49f-e529fd9a5eaf.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 6220 regions of interest ... OK: 3590 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/4/7/7/dataset_477b829d-2248-4f83-a49f-e529fd9a5eaf.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.69 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1767 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:16 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_157.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_157.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1767 (1767 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 3590 peaks identified in 1 samples.
 On average 3590 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 2.5-1138.9 seconds (0-19 minutes)
Mass range: 50.0321-963.0747 m/z
Peaks: 3590 (about 3590 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1767 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.805 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 11:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/4/d/9/dataset_4d98e102-d02a-4344-9771-604112fe0329.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 6293 regions of interest ... OK: 4264 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/4/d/9/dataset_4d98e102-d02a-4344-9771-604112fe0329.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.64 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1647 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:38:17 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: HU_neg_192.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  HU_neg_192.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1647 (1647 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 4264 peaks identified in 1 samples.
 On average 4264 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 6.2-1139.1 seconds (0.1-19 minutes)
Mass range: 50.025-963.0566 m/z
Peaks: 4264 (about 4264 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1647 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.884 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Job 12:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r  image '/tmp/tmp16fkh5mz/files/a/f/5/dataset_af53d62e-5e99-4d0b-9b0e-c82e3a416ec9.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method CentWave   ppm 3.0 peakwidth "c(5,20)"  snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE  peaklist FALSE        ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Detecting mass traces at 3 ppm ... OK
Detecting chromatographic peaks in 5041 regions of interest ... OK: 767 found.
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/a/f/5/dataset_af53d62e-5e99-4d0b-9b0e-c82e3a416ec9.dat
BPPARAM	1
method	CentWave
ppm	3
peakwidth	c(5, 20)
snthresh	10
prefilter	c(3, 5000)
mzCenterFun	wMean
integrate	1
mzdiff	-0.001
fitgauss	FALSE
noise	1000
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: 3 
 peakwidth: 5, 20 
 snthresh: 10 
 prefilter: 3, 5000 
 mzCenterFun: wMean 
 integrate: 1 
 mzdiff: -0.001 
 fitgauss: FALSE 
 noise: 1000 
 verboseColumns: FALSE 
 roiList length: 0 
 firstBaselineCheck TRUE 
 roiScales length: 0 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.78 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 2022 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Data loaded [Wed Oct  8 00:37:48 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  Blanc05.mzML 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S2022 (2022 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 767 peaks identified in 1 samples.
 On average 767 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 4.6-1139.1 seconds (0.1-19 minutes)
Mass range: 63.6207-989.2024 m/z
Peaks: 767 (about 767 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2022 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.434 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
filterSection	`{"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""}`
methods	`{"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"}`

Step 6: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/ae28a753a6f8/xcms_merge/xcms_merge.r  images 'c("/tmp/tmp16fkh5mz/files/8/e/a/dataset_8ea102f9-dbdf-49d8-bb15-0bbb209f0bc4.dat","/tmp/tmp16fkh5mz/files/3/3/f/dataset_33fc600e-a312-419a-b5c2-2450dcb30a05.dat","/tmp/tmp16fkh5mz/files/6/e/9/dataset_6e90457b-8571-48ec-b41f-ea9fd1c7994f.dat","/tmp/tmp16fkh5mz/files/0/a/2/dataset_0a2bad73-08e6-4bcd-a5b3-50ceca25a7ed.dat","/tmp/tmp16fkh5mz/files/e/b/a/dataset_ebae436a-5617-4757-a61e-5f415b597e67.dat","/tmp/tmp16fkh5mz/files/5/0/c/dataset_50cb819f-25ca-4feb-bf30-8bab5586bba1.dat","/tmp/tmp16fkh5mz/files/6/d/f/dataset_6df841b6-b893-4311-aa66-c3ddc49dcbee.dat","/tmp/tmp16fkh5mz/files/f/1/0/dataset_f10461ed-e0d2-45f5-902e-5ddd97f4cbd2.dat","/tmp/tmp16fkh5mz/files/1/c/3/dataset_1c35e971-787f-4a16-aedd-ed81e4648494.dat","/tmp/tmp16fkh5mz/files/2/8/7/dataset_28726df2-d9a6-44c9-a304-fc4bcd026c8b.dat","/tmp/tmp16fkh5mz/files/5/4/3/dataset_543cc338-1106-48e0-99d8-8652b4eabae7.dat","/tmp/tmp16fkh5mz/files/7/4/9/dataset_74913846-3ab4-491e-8586-84fb7ee91ab0.dat")'  sampleMetadata '/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat'

Exit Code:

```
0
```

Standard Error:

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

Standard Output:

R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	XSET MERGING...
Blanc05 
Blanc10 
Blanc16 
HU_neg_048 
HU_neg_090 
HU_neg_123 
HU_neg_157 
HU_neg_173 
HU_neg_192 
QC1_002 
QC1_008 
QC1_014 
	XSET PHENODATA SETTING...
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
                sample_name sample_group
Blanc05.mzML        Blanc05          blk
Blanc10.mzML        Blanc10          blk
Blanc16.mzML        Blanc16          blk
HU_neg_048.mzML  HU_neg_048       sample
HU_neg_090.mzML  HU_neg_090       sample
HU_neg_123.mzML  HU_neg_123       sample
HU_neg_157.mzML  HU_neg_157       sample
HU_neg_173.mzML  HU_neg_173       sample
HU_neg_192.mzML  HU_neg_192       sample
QC1_002.mzML        QC1_002           QC
QC1_008.mzML        QC1_008           QC
QC1_014.mzML        QC1_014           QC
MSn experiment data ("XCMSnExp")
Object size in memory: 6.31 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 34716 peaks identified in 12 samples.
 On average 2893 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
                sample_name sample_group  class
Blanc05.mzML        Blanc05          blk    blk
Blanc10.mzML        Blanc10          blk    blk
Blanc16.mzML        Blanc16          blk    blk
HU_neg_048.mzML  HU_neg_048       sample sample
HU_neg_090.mzML  HU_neg_090       sample sample
HU_neg_123.mzML  HU_neg_123       sample sample
HU_neg_157.mzML  HU_neg_157       sample sample
HU_neg_173.mzML  HU_neg_173       sample sample
HU_neg_192.mzML  HU_neg_192       sample sample
QC1_002.mzML        QC1_002           QC     QC
QC1_008.mzML        QC1_008           QC     QC
QC1_014.mzML        QC1_014           QC     QC
An "xcmsSet" object with 12 samples

Time range: 2-1139.5 seconds (0-19 minutes)
Mass range: 50.025-989.2024 m/z
Peaks: 34716 (about 2893 per sample)
Peak Groups: 0 
Sample classes: blk, sample, QC 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 8.47 MB


	SAVE RData

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

Step 7: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/3820e3f3b1cb/xcms_group/xcms_group.r image '/tmp/tmp16fkh5mz/files/1/6/5/dataset_165edffb-c53d-463f-b914-c6948add785e.dat'  method PeakDensity bw 5.0 minFraction 0.9 minSamples 1 binSize 0.01 maxFeatures 50   convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE       ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Processing 187837 mz slices ... OK
There were 50 or more warnings (use warnings() to see the first 50)
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/1/6/5/dataset_165edffb-c53d-463f-b914-c6948add785e.dat
method	PeakDensity
bw	5
minFraction	0.9
minSamples	1
binSize	0.01
maxFeatures	50
convertRTMinute	FALSE
numDigitsMZ	4
numDigitsRT	0
intval	into
naTOzero	TRUE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Perform the correspondence
Object of class:  PeakDensityParam 
Parameters:
 sampleGroups: character of length 12 
 bw: 5 
 minFraction: 0.9 
 minSamples: 1 
 binSize: 0.01 
 maxFeatures: 50 
		DRAW GRAPHICS
null device 
          1 


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 6.31 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: 0:1 - 18:60 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 34716 peaks identified in 12 samples.
 On average 2893 chromatographic peaks per sample.
Correspondence:
 method: chromatographic peak density 
 2228 features identified.
 Median mz range of features: 0.00028788
 Median rt range of features: 1.747


	xcmsSet OBJECT INFO
An "xcmsSet" object with 12 samples

Time range: 2-1139.5 seconds (0-19 minutes)
Mass range: 50.025-989.2024 m/z
Peaks: 34716 (about 2893 per sample)
Peak Groups: 2228 
Sample classes: blk, sample, QC 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 8.98 MB




	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
methods	`{"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.01", "bw": "5.0", "method": "PeakDensity", "minFraction": "0.9", "minSamples": "1"}`
peaklist	`{"__current_case__": 0, "convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"}`

Step 8: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/33c0ca93f3ee/xcms_retcor/xcms_retcor.r image '/tmp/tmp16fkh5mz/files/e/7/9/dataset_e79005de-6fb1-48ab-8ab7-5f4313351d72.dat'  method PeakGroups minFraction 0.7 extraPeaks 1 smooth loess span 0.2 family gaussian      ; return=$?; cat 'log.txt'; sh -c "exit $return"

Exit Code:

```
0
```

Standard Error:

Performing retention time correction using 673 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Warning message:
Adjusted retention times had to be re-adjusted for some files to ensure them being in the same order than the raw retention times. A call to 'dropAdjustedRtime' might thus fail to restore retention times of chromatographic peaks to their original values. Eventually consider to increase the value of the 'span' parameter. 
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
image	/tmp/tmp16fkh5mz/files/e/7/9/dataset_e79005de-6fb1-48ab-8ab7-5f4313351d72.dat
method	PeakGroups
minFraction	0.7
extraPeaks	1
smooth	loess
span	0.2
family	gaussian


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Alignment/Retention Time correction
Object of class:  PeakGroupsParam 
Parameters:
 minFraction: 0.7 
 extraPeaks: 1 
 smooth: loess 
 span: 0.2 
 family: gaussian 
 subset:  


		DRAW GRAPHICS
null device 
          1 


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 6.42 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: -1:58 - 19:2 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 34716 peaks identified in 12 samples.
 On average 2893 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 


	xcmsSet OBJECT INFO
An "xcmsSet" object with 12 samples

Time range: 1.1-1141.8 seconds (0-19 minutes)
Mass range: 50.025-989.2024 m/z
Peaks: 34716 (about 2893 per sample)
Peak Groups: 0 
Sample classes: blk, sample, QC 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 2039 
Profile settings: method = bin
                  step = 0.1

Memory usage: 8.58 MB




	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`
methods	`{"__current_case__": 0, "extraPeaks": "1", "method": "PeakGroups", "minFraction": "0.7", "smooth_cond": {"PeakGroupsSmoothLoessAdv": {"family": "gaussian", "span": "0.2"}, "__current_case__": 0, "smooth": "loess"}}`

Step 9: toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/e7c5811ec12f/checkformat/checkformat_wrapper.R dataMatrix_in "/tmp/tmp16fkh5mz/files/a/c/2/dataset_ac2cebe1-38a8-4cc4-b4c9-00aaff77eed5.dat" sampleMetadata_in "/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat" variableMetadata_in "/tmp/tmp16fkh5mz/files/4/0/a/dataset_40a5945e-793e-4a09-80f0-317888adae58.dat" makeNameL "FALSE"  dataMatrix_out "/tmp/tmp16fkh5mz/job_working_directory/000/42/outputs/dataset_82fc8192-3f20-4140-9094-3353e756b52a.dat" sampleMetadata_out "/tmp/tmp16fkh5mz/job_working_directory/000/42/outputs/dataset_b99f4e56-e3da-4144-8d3a-f3ed89a79939.dat" variableMetadata_out "/tmp/tmp16fkh5mz/job_working_directory/000/42/outputs/dataset_3cac9363-d808-4419-bf15-1fdabd1352e2.dat" information "/tmp/tmp16fkh5mz/job_working_directory/000/42/outputs/dataset_3edf276d-6676-4759-8835-bef43ef12451.dat"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
makeNameL	`"FALSE"`

Step 10: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/9291271ec4d9/xcms_plot_chromatogram/xcms_plot_chromatogram.r  images 'c("/tmp/tmp16fkh5mz/files/0/f/1/dataset_0f16453c-e9d9-474c-a3cf-053ff392e65a.dat")'  sampleMetadata '/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat'

Exit Code:

```
0
```

Standard Output:

	SESSION INFO
R version 4.0.5 (2021-03-31) 
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 0.20.44 	colorspace 2.0.1 	vctrs 0.3.8 	vsn 3.58.0 	utf8 1.2.1 	XML 3.99.0.6 	rlang 0.4.11 	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 1.30.15 	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 4.0.5 	tools 4.0.5 	bitops 1.0.7 	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 7.3.54 	ellipsis 0.3.2 	iterators 1.0.13 	R6 2.5.0 	MALDIquant 1.19.3 	compiler 4.0.5 	


	ARGUMENTS INFO
images	/tmp/tmp16fkh5mz/files/0/f/1/dataset_0f16453c-e9d9-474c-a3cf-053ff392e65a.dat
sampleMetadata	/tmp/tmp16fkh5mz/files/f/0/4/dataset_f04f426f-0479-467d-998b-6ac87a222578.dat


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Blanc05 Blanc10 Blanc16 HU_neg_048 HU_neg_090 HU_neg_123 HU_neg_157 HU_neg_173 HU_neg_192 QC1_002 QC1_008 QC1_014 
	XSET PHENODATA SETTING...


	MAIN PROCESSING INFO
		DRAW GRAPHICS
			Compute TIC
			Compute BPI
null device 
          1 
null device 
          1 


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 6.42 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 21878 
 MSn retention times: -1:58 - 19:2 minutes
- - - Processing information - - -
Concatenated [Wed Oct  8 00:40:45 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] Blanc05.mzML...  [12] QC1_014.mzML
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 34716 peaks identified in 12 samples.
 On average 2893 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups 


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d4337194a3de11f0a35e000d3a354906"`
chromInfo	`"/tmp/tmp16fkh5mz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

Other invocation details
- history_id
  - 5ae3493b5cdb304f
- history_state
  - error
- invocation_id
  - 5ae3493b5cdb304f
- invocation_state
  - scheduled
- workflow_id
  - 5ae3493b5cdb304f

Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2

6d55595

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2 #984

Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2 #984

Uh oh!

gxydevbot commented Oct 8, 2025

Uh oh!

github-actions bot commented Oct 8, 2025

Workflow invocation details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2 #984

Are you sure you want to change the base?

Updating workflows/metabolomics/lcms-preprocessing from 1.1 to 1.2 #984

Uh oh!

Conversation

gxydevbot commented Oct 8, 2025

Uh oh!

github-actions bot commented Oct 8, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant