Updating workflows/metabomics/gcms-metams from 0.1 to 0.2 #303

gxydevbot · 2023-11-27T04:31:25Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy1

The workflow release number has been updated from 0.1 to 0.2.

mvdbeek · 2023-11-27T09:32:10Z

@lecorguille can you have a look at this ? The test output is slightly different, but this is probably fine otherwhise

gxydevbot · 2024-09-23T14:30:56Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:17:00Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Mass-spectrometry__GCMS-with-metaMS.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

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

Step 3: toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy2:

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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/1/6/c/dataset_16c2b420-b3eb-495e-915f-a66500e3f345.dat' singlefile_sampleName 'alg11.mzData'   ; 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/tmpos9acjzu/files/1/6/c/dataset_16c2b420-b3eb-495e-915f-a66500e3f345.dat
singlefile_sampleName	alg11.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
alg11.mzData       alg11            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
alg11.mzData       alg11            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/9/4/0/dataset_940007ea-6916-4766-ae8e-7f8f76e12dab.dat' singlefile_sampleName 'alg2.mzData'   ; 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/tmpos9acjzu/files/9/4/0/dataset_940007ea-6916-4766-ae8e-7f8f76e12dab.dat
singlefile_sampleName	alg2.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg2.mzData        alg2            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg2.mzData        alg2            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/0/0/6/dataset_0061ce22-2ccc-4ce7-bd46-73c6f9c1bd59.dat' singlefile_sampleName 'alg3.mzData'   ; 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/tmpos9acjzu/files/0/0/6/dataset_0061ce22-2ccc-4ce7-bd46-73c6f9c1bd59.dat
singlefile_sampleName	alg3.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg3.mzData        alg3            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg3.mzData        alg3            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/a/2/a/dataset_a2a21a6a-88c1-4277-afcf-f52ca8c0d80a.dat' singlefile_sampleName 'alg7.mzData'   ; 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/tmpos9acjzu/files/a/2/a/dataset_a2a21a6a-88c1-4277-afcf-f52ca8c0d80a.dat
singlefile_sampleName	alg7.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg7.mzData        alg7            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg7.mzData        alg7            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/1/a/9/dataset_1a9f6e5c-7105-4e96-9c40-bf5b37358108.dat' singlefile_sampleName 'alg8.mzData'   ; 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/tmpos9acjzu/files/1/a/9/dataset_1a9f6e5c-7105-4e96-9c40-bf5b37358108.dat
singlefile_sampleName	alg8.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg8.mzData        alg8            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:54 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg8.mzData        alg8            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/5/3/8/dataset_538cf3ab-bfd3-4b04-bf8f-9a8fea00c230.dat' singlefile_sampleName 'alg9.mzData'   ; 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/tmpos9acjzu/files/5/3/8/dataset_538cf3ab-bfd3-4b04-bf8f-9a8fea00c230.dat
singlefile_sampleName	alg9.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg9.mzData        alg9            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:53 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg9.mzData        alg9            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+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/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/c/4/8/dataset_c48e9a78-a1e6-4b55-863f-ce785012bcb3.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/c/4/8/dataset_c48e9a78-a1e6-4b55-863f-ce785012bcb3.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 3025 peaks identified in 1 samples.
 On average 3025 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1196.7 seconds (10-19.9 minutes)
Mass range: 50.9572-449.1296 m/z
Peaks: 3025 (about 3025 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.773 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 2:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/1/1/9/dataset_119431a5-6d30-4851-abf7-65c7bf161f5c.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/1/1/9/dataset_119431a5-6d30-4851-abf7-65c7bf161f5c.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2268 peaks identified in 1 samples.
 On average 2268 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 600.8-1196.5 seconds (10-19.9 minutes)
Mass range: 50.2485-448.8367 m/z
Peaks: 2268 (about 2268 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.652 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 3:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/5/c/7/dataset_5c7b4fe5-682b-45f9-bcd7-7867c1803722.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/5/c/7/dataset_5c7b4fe5-682b-45f9-bcd7-7867c1803722.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2576 peaks identified in 1 samples.
 On average 2576 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.8-1197.5 seconds (10-20 minutes)
Mass range: 50.1621-448.9793 m/z
Peaks: 2576 (about 2576 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.701 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 4:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/d/d/2/dataset_dd2c6a38-6244-4e2c-b6eb-82c28f7502d5.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/d/d/2/dataset_dd2c6a38-6244-4e2c-b6eb-82c28f7502d5.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:42 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2466 peaks identified in 1 samples.
 On average 2466 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9493-449.2975 m/z
Peaks: 2466 (about 2466 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.684 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 5:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/7/9/2/dataset_79261624-3ac0-44b1-9a4f-340f8d321aae.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/7/9/2/dataset_79261624-3ac0-44b1-9a4f-340f8d321aae.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:54 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2544 peaks identified in 1 samples.
 On average 2544 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 601.5-1197 seconds (10-20 minutes)
Mass range: 50.9637-449.1156 m/z
Peaks: 2544 (about 2544 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.696 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 6:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmpos9acjzu/files/8/6/5/dataset_8659948b-39bf-4cc6-9e36-0f38bf5f0321.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpos9acjzu/files/8/6/5/dataset_8659948b-39bf-4cc6-9e36-0f38bf5f0321.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Sep 23 15:08:53 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2765 peaks identified in 1 samples.
 On average 2765 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9528-448.9991 m/z
Peaks: 2765 (about 2765 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.732 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Step 5: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+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/xcms_plot_chromatogram/c8bef8f6a1cb/xcms_plot_chromatogram///xcms_plot_chromatogram.r  images 'c("/tmp/tmpos9acjzu/files/a/5/3/dataset_a53aff8b-470f-4a65-a784-4703c03ea4ed.dat","/tmp/tmpos9acjzu/files/5/6/1/dataset_561737f9-9411-4e4a-99d2-bcad0d1b51a6.dat","/tmp/tmpos9acjzu/files/7/f/c/dataset_7fc73a69-9243-49cb-a466-a1269720586b.dat","/tmp/tmpos9acjzu/files/1/6/9/dataset_1693436e-02a2-45c7-a434-63a4e45086be.dat","/tmp/tmpos9acjzu/files/4/f/3/dataset_4f3b8a01-c253-4680-b4b1-941dd8da4d1b.dat","/tmp/tmpos9acjzu/files/1/b/f/dataset_1bfc6127-9636-4175-b9a3-2c0f17e4aadd.dat")'  sampleMetadata '/tmp/tmpos9acjzu/files/1/e/c/dataset_1ec4ed05-fdd1-4847-86f2-825eed3fc8bd.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	c("/tmp/tmpos9acjzu/files/a/5/3/dataset_a53aff8b-470f-4a65-a784-4703c03ea4ed.dat", "/tmp/tmpos9acjzu/files/5/6/1/dataset_561737f9-9411-4e4a-99d2-bcad0d1b51a6.dat", "/tmp/tmpos9acjzu/files/7/f/c/dataset_7fc73a69-9243-49cb-a466-a1269720586b.dat", "/tmp/tmpos9acjzu/files/1/6/9/dataset_1693436e-02a2-45c7-a434-63a4e45086be.dat", "/tmp/tmpos9acjzu/files/4/f/3/dataset_4f3b8a01-c253-4680-b4b1-941dd8da4d1b.dat", "/tmp/tmpos9acjzu/files/1/b/f/dataset_1bfc6127-9636-4175-b9a3-2c0f17e4aadd.dat")
sampleMetadata	/tmp/tmpos9acjzu/files/1/e/c/dataset_1ec4ed05-fdd1-4847-86f2-825eed3fc8bd.dat


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Mon Sep 23 15:09:58 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

Step 6: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+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/xcms_merge/6d475a389abc/xcms_merge//xcms_merge.r  images 'c("/tmp/tmpos9acjzu/files/a/5/3/dataset_a53aff8b-470f-4a65-a784-4703c03ea4ed.dat","/tmp/tmpos9acjzu/files/5/6/1/dataset_561737f9-9411-4e4a-99d2-bcad0d1b51a6.dat","/tmp/tmpos9acjzu/files/7/f/c/dataset_7fc73a69-9243-49cb-a466-a1269720586b.dat","/tmp/tmpos9acjzu/files/1/6/9/dataset_1693436e-02a2-45c7-a434-63a4e45086be.dat","/tmp/tmpos9acjzu/files/4/f/3/dataset_4f3b8a01-c253-4680-b4b1-941dd8da4d1b.dat","/tmp/tmpos9acjzu/files/1/b/f/dataset_1bfc6127-9636-4175-b9a3-2c0f17e4aadd.dat")'  sampleMetadata '/tmp/tmpos9acjzu/files/1/e/c/dataset_1ec4ed05-fdd1-4847-86f2-825eed3fc8bd.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...
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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


	XCMSnExp OBJECT INFO
             sample_name   sample_group
alg11.mzData       alg11 FWS_100perNaCl
alg2.mzData         alg2            SWS
alg3.mzData         alg3            SWS
alg7.mzData         alg7  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl
MSn experiment data ("XCMSnExp")
Object size in memory: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Mon Sep 23 15:09:58 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
             sample_name   sample_group          class
alg11.mzData       alg11 FWS_100perNaCl FWS_100perNaCl
alg2.mzData         alg2            SWS            SWS
alg3.mzData         alg3            SWS            SWS
alg7.mzData         alg7  FWS_5percNaCL  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl FWS_100perNaCl
An "xcmsSet" object with 6 samples

Time range: 599.8-1197.7 seconds (10-20 minutes)
Mass range: 50.1621-449.2975 m/z
Peaks: 15644 (about 2607 per sample)
Peak Groups: 0 
Sample classes: FWS_100perNaCl, SWS, FWS_5percNaCL 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 4.2 MB


	SAVE RData

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/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/yguitton/metams_rungc/metams_runGC/3.0.0+metaMS1.24.0-galaxy0:

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/yguitton/metams_rungc/93508ea69eb5/metams_rungc///metaMS_runGC.r  singlefile_galaxyPath '/tmp/tmpos9acjzu/files/3/5/9/dataset_359ba56b-022b-417a-bf95-3c22951189ad.dat' singlefile_sampleName 'xset.merged.RData'  settings "User_defined" rtdiff 0.05 minfeat 5 simthreshold 0.7 minclassfraction 0.5 minclasssize 3 rtrange "NULL" ri "NULL" rishift "none" db "NULL" nSlaves ${GALAXY_SLOTS:-1}

Exit Code:

```
0
```

Standard Error:

Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
< -------- Experiment of 6 samples ------------------------------------- >
< -------- Instrument: GALAXY.GC --------------------------------------- >
< -------- No annotation performed ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >

Standard Output:

	SESSION INFO

R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	stringr 1.4.1 	metaMS 1.24.0 	CAMERA 1.44.0 	xcms 3.10.0 	MSnbase 2.14.1 	ProtGenerics 1.20.0 	S4Vectors 0.26.0 	mzR 2.22.0 	Rcpp 1.0.9 	BiocParallel 1.22.0 	Biobase 2.48.0 	BiocGenerics 0.34.0 	
Other loaded packages:
bitops 1.0.7 	matrixStats 0.62.0 	doParallel 1.0.17 	RColorBrewer 1.1.3 	GenomeInfoDb 1.24.0 	tools 4.0.5 	backports 1.4.1 	utf8 1.2.2 	R6 2.5.1 	affyio 1.58.0 	rpart 4.1.16 	Hmisc 4.7.1 	colorspace 2.0.3 	nnet 7.3.17 	gridExtra 2.3 	compiler 4.0.5 	MassSpecWavelet 1.54.0 	preprocessCore 1.50.0 	graph 1.66.0 	cli 3.4.1 	htmlTable 2.4.1 	DelayedArray 0.14.0 	scales 1.2.1 	checkmate 2.1.0 	DEoptimR 1.0.11 	robustbase 0.95.0 	affy 1.66.0 	RBGL 1.64.0 	digest 0.6.29 	foreign 0.8.82 	XVector 0.28.0 	base64enc 0.1.3 	jpeg 0.1.9 	pkgconfig 2.0.3 	htmltools 0.5.3 	fastmap 1.1.0 	limma 3.44.1 	htmlwidgets 1.5.4 	rlang 1.0.6 	rstudioapi 0.14 	impute 1.62.0 	mzID 1.26.0 	RCurl 1.98.1.8 	magrittr 2.0.3 	GenomeInfoDbData 1.2.4 	Formula 1.2.4 	interp 1.1.3 	MALDIquant 1.21 	Matrix 1.4.1 	munsell 0.5.0 	fansi 1.0.3 	lifecycle 1.0.2 	vsn 3.56.0 	stringi 1.7.8 	MASS 7.3.58.1 	SummarizedExperiment 1.18.1 	zlibbioc 1.34.0 	plyr 1.8.7 	grid 4.0.5 	deldir 1.0.6 	lattice 0.20.45 	splines 4.0.5 	knitr 1.40 	pillar 1.8.1 	igraph 1.3.1 	GenomicRanges 1.40.0 	codetools 0.2.18 	XML 3.99.0.10 	glue 1.6.2 	latticeExtra 0.6.30 	pcaMethods 1.80.0 	data.table 1.14.2 	BiocManager 1.30.18 	png 0.1.7 	vctrs 0.4.1 	foreach 1.5.2 	gtable 0.3.1 	RANN 2.6.1 	ggplot2 3.3.6 	xfun 0.33 	ncdf4 1.19 	survival 3.4.0 	tibble 3.1.8 	iterators 1.0.14 	IRanges 2.22.1 	cluster 2.1.3 	



Start of the 'metaMS:runGC' Galaxy module call: Mon 23 Sep 2024 15:12:48


	ARGUMENTS PROCESSING INFO

                      value                                                                          
singlefile_galaxyPath "/tmp/tmpos9acjzu/files/3/5/9/dataset_359ba56b-022b-417a-bf95-3c22951189ad.dat"
singlefile_sampleName "xset.merged.RData"                                                            
settings              "User_defined"                                                                 
rtdiff                "0.05"                                                                         
minfeat               "5"                                                                            
simthreshold          "0.7"                                                                          
minclassfraction      "0.5"                                                                          
minclasssize          "3"                                                                            
rtrange               "NULL"                                                                         
ri                    "NULL"                                                                         
rishift               "none"                                                                         
db                    "NULL"                                                                         
nSlaves               "1"                                                                            


	ARGUMENTS PROCESSING INFO

Using user's parameters
rtrange= 


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE

Loading datas from XCMS files...
Process xsAnnotate with CAMERA package...
Process runGC with metaMS package...

Formal class 'metaMSsettings' [package "metaMS"] with 30 slots
  ..@ protocolName                      : chr "GALAXY.GC"
  ..@ chrom                             : chr "GC"
  ..@ PeakPicking                       :List of 7
  .. ..$ method  : chr "matchedFilter"
  .. ..$ step    : num 0.5
  .. ..$ steps   : num 2
  .. ..$ mzdiff  : num 0.5
  .. ..$ fwhm    : num 5
  .. ..$ snthresh: num 2
  .. ..$ max     : num 500
  ..@ Alignment                         : list()
  ..@ CAMERA                            :List of 1
  .. ..$ perfwhm: num 1
  ..@ match2DB.rtdiff                   : num 0.05
  ..@ match2DB.minfeat                  : num 5
  ..@ match2DB.rtval                    : num(0) 
  ..@ match2DB.mzdiff                   : num(0) 
  ..@ match2DB.ppm                      : num(0) 
  ..@ match2DB.simthresh                : num 0.7
  ..@ match2DB.timeComparison           : chr "rt"
  ..@ match2DB.RIdiff                   : num 5
  ..@ DBconstruction.minfeat            : num 5
  ..@ DBconstruction.rttol              : num 0.05
  ..@ DBconstruction.mztol              : num(0) 
  ..@ DBconstruction.minintens          : num 0
  ..@ DBconstruction.intensityMeasure   : chr "maxo"
  ..@ DBconstruction.DBthreshold        : num 0.8
  ..@ matchIrrelevants.irrelevantClasses: chr(0) 
  ..@ matchIrrelevants.simthresh        : num(0) 
  ..@ matchIrrelevants.timeComparison   : chr(0) 
  ..@ matchIrrelevants.RIdiff           : num(0) 
  ..@ matchIrrelevants.rtdiff           : num(0) 
  ..@ betweenSamples.min.class.fraction : num 0.5
  ..@ betweenSamples.min.class.size     : num 3
  ..@ betweenSamples.timeComparison     : chr "rt"
  ..@ betweenSamples.rtdiff             : num 0.05
  ..@ betweenSamples.RIdiff             : num 2
  ..@ betweenSamples.simthresh          : num 0.7
NULL

Generating peakTable file	.	.	.	OK
Generating dataMatrix file	.	.	.	OK
Generating variableMetadata file	.	.	OK
Generating sampleMetadata file	.	.	.	OK
Generating 41 peakspectra in peakspectra.msp file

End of 'metaMS:runGC' Galaxy module call: 2024-09-23 15:12:51

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"rdata.xcms.findchrompeaks"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
options_rifilter	`{"__current_case__": 1, "option": "false"}`
settings	`{"__current_case__": 1, "minclassfraction": "0.5", "minclasssize": "3", "minfeat": "5", "options_db": {"__current_case__": 1, "option": "hide"}, "options_ri": {"__current_case__": 1, "option": "hide"}, "options_rtrange": {"__current_case__": 1, "option": "hide"}, "rtdiff": "0.05", "setting": "usersettings", "simthreshold": "0.7"}`

Step 8: 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/tmpos9acjzu/files/a/7/b/dataset_a7ba125f-b7ef-4ff7-9e38-b9a3ce9d007f.dat" sampleMetadata_in "/tmp/tmpos9acjzu/files/1/e/c/dataset_1ec4ed05-fdd1-4847-86f2-825eed3fc8bd.dat" variableMetadata_in "/tmp/tmpos9acjzu/files/8/4/2/dataset_842698ee-52e5-4aa4-b967-e64e2c547cfe.dat" makeNameL "FALSE"  dataMatrix_out "/tmp/tmpos9acjzu/job_working_directory/000/23/outputs/dataset_83ffc1c2-340f-4a53-96a4-63d24345d5ac.dat" sampleMetadata_out "/tmp/tmpos9acjzu/job_working_directory/000/23/outputs/dataset_faec5c26-4038-4702-a08c-ee2fc73cf250.dat" variableMetadata_out "/tmp/tmpos9acjzu/job_working_directory/000/23/outputs/dataset_a6a121f8-6715-4159-b0c4-d3861eb613eb.dat" information "/tmp/tmpos9acjzu/job_working_directory/000/23/outputs/dataset_3d5e5449-9828-4e1e-b2da-fc11c363dbd2.dat"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
chromInfo	`"/tmp/tmpos9acjzu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
makeNameL	`"FALSE"`

Step 9: toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/5526f8258e8a/multivariate/multivariate_wrapper.R  dataMatrix_in "/tmp/tmpos9acjzu/files/8/3/f/dataset_83ffc1c2-340f-4a53-96a4-63d24345d5ac.dat" sampleMetadata_in "/tmp/tmpos9acjzu/files/f/a/e/dataset_faec5c26-4038-4702-a08c-ee2fc73cf250.dat" variableMetadata_in "/tmp/tmpos9acjzu/files/a/6/a/dataset_a6a121f8-6715-4159-b0c4-d3861eb613eb.dat"  respC "none" predI "NA" orthoI "0" testL "FALSE"  typeC "summary" parAsColC "class" parCexN "0.8" parPc1I "1" parPc2I "2" parMahalC "NA" parLabVc "none"  algoC "default" crossvalI "3" log10L "FALSE" permI "20" scaleC "standard"  sampleMetadata_out "/tmp/tmpos9acjzu/job_working_directory/000/24/outputs/dataset_3a9cfef4-c82a-4988-bdb5-ccea4171cb4c.dat" variableMetadata_out "/tmp/tmpos9acjzu/job_working_directory/000/24/outputs/dataset_641550ab-1303-45e1-8d19-036305cc184a.dat" figure "/tmp/tmpos9acjzu/job_working_directory/000/24/outputs/dataset_821928f0-d311-41ad-a409-ee2019f74e68.dat" information "/tmp/tmpos9acjzu/job_working_directory/000/24/outputs/dataset_c4261b21-3168-4f6b-8b8a-10996e6774bd.dat"

Exit Code:

```
127
```

Standard Error:

Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9fad5ada79bd11efa6a3f11b37b92d10"`
advCpt	`{"__current_case__": 1, "algoC": "default", "crossvalI": "3", "log10L": "FALSE", "opcC": "full", "permI": "20", "scaleC": "standard"}`
advGph	`{"__current_case__": 1, "opgC": "full", "parAsColC": "class", "parCexN": "0.8", "parLabVc": "none", "parMahalC": "NA", "parPc1I": "1", "parPc2I": "2", "typeC": "summary"}`
chromInfo	`"/tmp/tmpos9acjzu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
orthoI	`"0"`
predI	`"NA"`
respC	`"none"`
save_rdata	`false`
testL	`"FALSE"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - ca432be4c8d6da0d
- history_state
  - error
- invocation_id
  - ca432be4c8d6da0d
- invocation_state
  - scheduled
- workflow_id
  - ca432be4c8d6da0d

gxydevbot · 2024-09-24T14:07:47Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-24T14:22:55Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Mass-spectrometry__GCMS-with-metaMS.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

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

Step 3: toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy2:

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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/5/e/a/dataset_5eae3bdf-e367-46cf-8f92-c2778dc75c68.dat' singlefile_sampleName 'alg11.mzData'   ; 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/tmp77stj8bh/files/5/e/a/dataset_5eae3bdf-e367-46cf-8f92-c2778dc75c68.dat
singlefile_sampleName	alg11.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
alg11.mzData       alg11            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
alg11.mzData       alg11            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/d/8/1/dataset_d81cada1-bece-4ae6-8e21-2ffe74184560.dat' singlefile_sampleName 'alg2.mzData'   ; 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/tmp77stj8bh/files/d/8/1/dataset_d81cada1-bece-4ae6-8e21-2ffe74184560.dat
singlefile_sampleName	alg2.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg2.mzData        alg2            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:55 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg2.mzData        alg2            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/2/7/b/dataset_27bf6421-55c2-4d54-aa30-091dedb47899.dat' singlefile_sampleName 'alg3.mzData'   ; 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/tmp77stj8bh/files/2/7/b/dataset_27bf6421-55c2-4d54-aa30-091dedb47899.dat
singlefile_sampleName	alg3.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg3.mzData        alg3            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg3.mzData        alg3            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/b/6/4/dataset_b644e9bc-5bbf-4fdd-9fbe-b695d872f22f.dat' singlefile_sampleName 'alg7.mzData'   ; 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/tmp77stj8bh/files/b/6/4/dataset_b644e9bc-5bbf-4fdd-9fbe-b695d872f22f.dat
singlefile_sampleName	alg7.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg7.mzData        alg7            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg7.mzData        alg7            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/c/3/b/dataset_c3beddcc-4a37-480c-b0b2-2c3f7f2e3570.dat' singlefile_sampleName 'alg8.mzData'   ; 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/tmp77stj8bh/files/c/3/b/dataset_c3beddcc-4a37-480c-b0b2-2c3f7f2e3570.dat
singlefile_sampleName	alg8.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg8.mzData        alg8            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:16:08 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg8.mzData        alg8            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/6de175c1f6ef/msnbase_readmsdata//msnbase_readmsdata.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/e/e/9/dataset_ee9593e4-6678-473e-9c3a-a80947190b4f.dat' singlefile_sampleName 'alg9.mzData'   ; 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/tmp77stj8bh/files/e/e/9/dataset_ee9593e4-6678-473e-9c3a-a80947190b4f.dat
singlefile_sampleName	alg9.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg9.mzData        alg9            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:16:08 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg9.mzData        alg9            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+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/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/f/2/9/dataset_f29526f9-ddc9-4cf2-8359-0006afd2314c.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/f/2/9/dataset_f29526f9-ddc9-4cf2-8359-0006afd2314c.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 3025 peaks identified in 1 samples.
 On average 3025 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1196.7 seconds (10-19.9 minutes)
Mass range: 50.9572-449.1296 m/z
Peaks: 3025 (about 3025 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.773 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 2:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/2/7/7/dataset_277eb761-147f-4e76-9b6e-9adcadcc1027.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/2/7/7/dataset_277eb761-147f-4e76-9b6e-9adcadcc1027.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:55 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2268 peaks identified in 1 samples.
 On average 2268 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 600.8-1196.5 seconds (10-19.9 minutes)
Mass range: 50.2485-448.8367 m/z
Peaks: 2268 (about 2268 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.652 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 3:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/6/1/9/dataset_61949b2c-938c-4734-8df4-8a6b00f3ec29.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/6/1/9/dataset_61949b2c-938c-4734-8df4-8a6b00f3ec29.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2576 peaks identified in 1 samples.
 On average 2576 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.8-1197.5 seconds (10-20 minutes)
Mass range: 50.1621-448.9793 m/z
Peaks: 2576 (about 2576 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.701 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 4:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/0/0/f/dataset_00f2157f-c9de-4755-99fb-7dd40ce8a1ef.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/0/0/f/dataset_00f2157f-c9de-4755-99fb-7dd40ce8a1ef.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:15:56 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2466 peaks identified in 1 samples.
 On average 2466 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9493-449.2975 m/z
Peaks: 2466 (about 2466 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.684 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 5:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/2/0/9/dataset_20920ba4-60e4-4c53-ab60-fa1d4a542068.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/2/0/9/dataset_20920ba4-60e4-4c53-ab60-fa1d4a542068.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:16:08 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2544 peaks identified in 1 samples.
 On average 2544 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 601.5-1197 seconds (10-20 minutes)
Mass range: 50.9637-449.1156 m/z
Peaks: 2544 (about 2544 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.696 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Job 6:

Job state is ok

Command Line:

LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/6550698fe60f/xcms_xcmsset//xcms_xcmsSet.r  image '/tmp/tmp77stj8bh/files/e/a/c/dataset_eac8ac6b-e2e8-433f-9049-b1825dc48c1f.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmp77stj8bh/files/e/a/c/dataset_eac8ac6b-e2e8-433f-9049-b1825dc48c1f.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Tue Sep 24 14:16:08 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2765 peaks identified in 1 samples.
 On average 2765 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9528-448.9991 m/z
Peaks: 2765 (about 2765 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.732 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Step 5: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+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/xcms_plot_chromatogram/c8bef8f6a1cb/xcms_plot_chromatogram///xcms_plot_chromatogram.r  images 'c("/tmp/tmp77stj8bh/files/1/7/1/dataset_171c15fa-58ec-4fcf-a644-1e88f08b05d6.dat","/tmp/tmp77stj8bh/files/c/4/0/dataset_c4048b52-1930-42c2-a8a6-952969564882.dat","/tmp/tmp77stj8bh/files/0/d/7/dataset_0d71a689-8f48-4145-bda7-0561066a5a01.dat","/tmp/tmp77stj8bh/files/2/5/8/dataset_258d9a6d-5b0f-48ad-8432-e535483810ef.dat","/tmp/tmp77stj8bh/files/c/5/3/dataset_c530db0b-4331-42f7-a90e-17bc4e8c051a.dat","/tmp/tmp77stj8bh/files/d/9/8/dataset_d98c32a8-d4af-4f55-9a23-a7748dce7d70.dat")'  sampleMetadata '/tmp/tmp77stj8bh/files/7/d/9/dataset_7d96ea15-6ec5-4e9f-9094-54ac7c5defcf.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	c("/tmp/tmp77stj8bh/files/1/7/1/dataset_171c15fa-58ec-4fcf-a644-1e88f08b05d6.dat", "/tmp/tmp77stj8bh/files/c/4/0/dataset_c4048b52-1930-42c2-a8a6-952969564882.dat", "/tmp/tmp77stj8bh/files/0/d/7/dataset_0d71a689-8f48-4145-bda7-0561066a5a01.dat", "/tmp/tmp77stj8bh/files/2/5/8/dataset_258d9a6d-5b0f-48ad-8432-e535483810ef.dat", "/tmp/tmp77stj8bh/files/c/5/3/dataset_c530db0b-4331-42f7-a90e-17bc4e8c051a.dat", "/tmp/tmp77stj8bh/files/d/9/8/dataset_d98c32a8-d4af-4f55-9a23-a7748dce7d70.dat")
sampleMetadata	/tmp/tmp77stj8bh/files/7/d/9/dataset_7d96ea15-6ec5-4e9f-9094-54ac7c5defcf.dat


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Tue Sep 24 14:17:14 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

Step 6: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+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/xcms_merge/6d475a389abc/xcms_merge//xcms_merge.r  images 'c("/tmp/tmp77stj8bh/files/1/7/1/dataset_171c15fa-58ec-4fcf-a644-1e88f08b05d6.dat","/tmp/tmp77stj8bh/files/c/4/0/dataset_c4048b52-1930-42c2-a8a6-952969564882.dat","/tmp/tmp77stj8bh/files/0/d/7/dataset_0d71a689-8f48-4145-bda7-0561066a5a01.dat","/tmp/tmp77stj8bh/files/2/5/8/dataset_258d9a6d-5b0f-48ad-8432-e535483810ef.dat","/tmp/tmp77stj8bh/files/c/5/3/dataset_c530db0b-4331-42f7-a90e-17bc4e8c051a.dat","/tmp/tmp77stj8bh/files/d/9/8/dataset_d98c32a8-d4af-4f55-9a23-a7748dce7d70.dat")'  sampleMetadata '/tmp/tmp77stj8bh/files/7/d/9/dataset_7d96ea15-6ec5-4e9f-9094-54ac7c5defcf.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...
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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


	XCMSnExp OBJECT INFO
             sample_name   sample_group
alg11.mzData       alg11 FWS_100perNaCl
alg2.mzData         alg2            SWS
alg3.mzData         alg3            SWS
alg7.mzData         alg7  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl
MSn experiment data ("XCMSnExp")
Object size in memory: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Tue Sep 24 14:17:14 2024] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
             sample_name   sample_group          class
alg11.mzData       alg11 FWS_100perNaCl FWS_100perNaCl
alg2.mzData         alg2            SWS            SWS
alg3.mzData         alg3            SWS            SWS
alg7.mzData         alg7  FWS_5percNaCL  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl FWS_100perNaCl
An "xcmsSet" object with 6 samples

Time range: 599.8-1197.7 seconds (10-20 minutes)
Mass range: 50.1621-449.2975 m/z
Peaks: 15644 (about 2607 per sample)
Peak Groups: 0 
Sample classes: FWS_100perNaCl, SWS, FWS_5percNaCL 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 4.2 MB


	SAVE RData

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/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/yguitton/metams_rungc/metams_runGC/3.0.0+metaMS1.24.0-galaxy0:

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/yguitton/metams_rungc/93508ea69eb5/metams_rungc///metaMS_runGC.r  singlefile_galaxyPath '/tmp/tmp77stj8bh/files/7/2/6/dataset_726bb926-d427-4865-b7b0-c7fed8176384.dat' singlefile_sampleName 'xset.merged.RData'  settings "User_defined" rtdiff 0.05 minfeat 5 simthreshold 0.7 minclassfraction 0.5 minclasssize 3 rtrange "NULL" ri "NULL" rishift "none" db "NULL" nSlaves ${GALAXY_SLOTS:-1}

Exit Code:

```
0
```

Standard Error:

Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
< -------- Experiment of 6 samples ------------------------------------- >
< -------- Instrument: GALAXY.GC --------------------------------------- >
< -------- No annotation performed ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >

Standard Output:

	SESSION INFO

R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	stringr 1.4.1 	metaMS 1.24.0 	CAMERA 1.44.0 	xcms 3.10.0 	MSnbase 2.14.1 	ProtGenerics 1.20.0 	S4Vectors 0.26.0 	mzR 2.22.0 	Rcpp 1.0.9 	BiocParallel 1.22.0 	Biobase 2.48.0 	BiocGenerics 0.34.0 	
Other loaded packages:
bitops 1.0.7 	matrixStats 0.62.0 	doParallel 1.0.17 	RColorBrewer 1.1.3 	GenomeInfoDb 1.24.0 	tools 4.0.5 	backports 1.4.1 	utf8 1.2.2 	R6 2.5.1 	affyio 1.58.0 	rpart 4.1.16 	Hmisc 4.7.1 	colorspace 2.0.3 	nnet 7.3.17 	gridExtra 2.3 	compiler 4.0.5 	MassSpecWavelet 1.54.0 	preprocessCore 1.50.0 	graph 1.66.0 	cli 3.4.1 	htmlTable 2.4.1 	DelayedArray 0.14.0 	scales 1.2.1 	checkmate 2.1.0 	DEoptimR 1.0.11 	robustbase 0.95.0 	affy 1.66.0 	RBGL 1.64.0 	digest 0.6.29 	foreign 0.8.82 	XVector 0.28.0 	base64enc 0.1.3 	jpeg 0.1.9 	pkgconfig 2.0.3 	htmltools 0.5.3 	fastmap 1.1.0 	limma 3.44.1 	htmlwidgets 1.5.4 	rlang 1.0.6 	rstudioapi 0.14 	impute 1.62.0 	mzID 1.26.0 	RCurl 1.98.1.8 	magrittr 2.0.3 	GenomeInfoDbData 1.2.4 	Formula 1.2.4 	interp 1.1.3 	MALDIquant 1.21 	Matrix 1.4.1 	munsell 0.5.0 	fansi 1.0.3 	lifecycle 1.0.2 	vsn 3.56.0 	stringi 1.7.8 	MASS 7.3.58.1 	SummarizedExperiment 1.18.1 	zlibbioc 1.34.0 	plyr 1.8.7 	grid 4.0.5 	deldir 1.0.6 	lattice 0.20.45 	splines 4.0.5 	knitr 1.40 	pillar 1.8.1 	igraph 1.3.1 	GenomicRanges 1.40.0 	codetools 0.2.18 	XML 3.99.0.10 	glue 1.6.2 	latticeExtra 0.6.30 	pcaMethods 1.80.0 	data.table 1.14.2 	BiocManager 1.30.18 	png 0.1.7 	vctrs 0.4.1 	foreach 1.5.2 	gtable 0.3.1 	RANN 2.6.1 	ggplot2 3.3.6 	xfun 0.33 	ncdf4 1.19 	survival 3.4.0 	tibble 3.1.8 	iterators 1.0.14 	IRanges 2.22.1 	cluster 2.1.3 	



Start of the 'metaMS:runGC' Galaxy module call: Tue 24 Sep 2024 14:20:04


	ARGUMENTS PROCESSING INFO

                      value                                                                          
singlefile_galaxyPath "/tmp/tmp77stj8bh/files/7/2/6/dataset_726bb926-d427-4865-b7b0-c7fed8176384.dat"
singlefile_sampleName "xset.merged.RData"                                                            
settings              "User_defined"                                                                 
rtdiff                "0.05"                                                                         
minfeat               "5"                                                                            
simthreshold          "0.7"                                                                          
minclassfraction      "0.5"                                                                          
minclasssize          "3"                                                                            
rtrange               "NULL"                                                                         
ri                    "NULL"                                                                         
rishift               "none"                                                                         
db                    "NULL"                                                                         
nSlaves               "1"                                                                            


	ARGUMENTS PROCESSING INFO

Using user's parameters
rtrange= 


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE

Loading datas from XCMS files...
Process xsAnnotate with CAMERA package...
Process runGC with metaMS package...

Formal class 'metaMSsettings' [package "metaMS"] with 30 slots
  ..@ protocolName                      : chr "GALAXY.GC"
  ..@ chrom                             : chr "GC"
  ..@ PeakPicking                       :List of 7
  .. ..$ method  : chr "matchedFilter"
  .. ..$ step    : num 0.5
  .. ..$ steps   : num 2
  .. ..$ mzdiff  : num 0.5
  .. ..$ fwhm    : num 5
  .. ..$ snthresh: num 2
  .. ..$ max     : num 500
  ..@ Alignment                         : list()
  ..@ CAMERA                            :List of 1
  .. ..$ perfwhm: num 1
  ..@ match2DB.rtdiff                   : num 0.05
  ..@ match2DB.minfeat                  : num 5
  ..@ match2DB.rtval                    : num(0) 
  ..@ match2DB.mzdiff                   : num(0) 
  ..@ match2DB.ppm                      : num(0) 
  ..@ match2DB.simthresh                : num 0.7
  ..@ match2DB.timeComparison           : chr "rt"
  ..@ match2DB.RIdiff                   : num 5
  ..@ DBconstruction.minfeat            : num 5
  ..@ DBconstruction.rttol              : num 0.05
  ..@ DBconstruction.mztol              : num(0) 
  ..@ DBconstruction.minintens          : num 0
  ..@ DBconstruction.intensityMeasure   : chr "maxo"
  ..@ DBconstruction.DBthreshold        : num 0.8
  ..@ matchIrrelevants.irrelevantClasses: chr(0) 
  ..@ matchIrrelevants.simthresh        : num(0) 
  ..@ matchIrrelevants.timeComparison   : chr(0) 
  ..@ matchIrrelevants.RIdiff           : num(0) 
  ..@ matchIrrelevants.rtdiff           : num(0) 
  ..@ betweenSamples.min.class.fraction : num 0.5
  ..@ betweenSamples.min.class.size     : num 3
  ..@ betweenSamples.timeComparison     : chr "rt"
  ..@ betweenSamples.rtdiff             : num 0.05
  ..@ betweenSamples.RIdiff             : num 2
  ..@ betweenSamples.simthresh          : num 0.7
NULL

Generating peakTable file	.	.	.	OK
Generating dataMatrix file	.	.	.	OK
Generating variableMetadata file	.	.	OK
Generating sampleMetadata file	.	.	.	OK
Generating 41 peakspectra in peakspectra.msp file

End of 'metaMS:runGC' Galaxy module call: 2024-09-24 14:20:07

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"rdata.xcms.findchrompeaks"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
options_rifilter	`{"__current_case__": 1, "option": "false"}`
settings	`{"__current_case__": 1, "minclassfraction": "0.5", "minclasssize": "3", "minfeat": "5", "options_db": {"__current_case__": 1, "option": "hide"}, "options_ri": {"__current_case__": 1, "option": "hide"}, "options_rtrange": {"__current_case__": 1, "option": "hide"}, "rtdiff": "0.05", "setting": "usersettings", "simthreshold": "0.7"}`

Step 8: 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/tmp77stj8bh/files/7/7/6/dataset_7762e966-9bb8-4d07-a52c-2c5136a77bab.dat" sampleMetadata_in "/tmp/tmp77stj8bh/files/7/d/9/dataset_7d96ea15-6ec5-4e9f-9094-54ac7c5defcf.dat" variableMetadata_in "/tmp/tmp77stj8bh/files/4/f/5/dataset_4f5c240e-fd60-4b78-90d4-e6874fe72345.dat" makeNameL "FALSE"  dataMatrix_out "/tmp/tmp77stj8bh/job_working_directory/000/23/outputs/dataset_d7da6ac8-70f7-440c-b148-48ccda4e1a00.dat" sampleMetadata_out "/tmp/tmp77stj8bh/job_working_directory/000/23/outputs/dataset_e0266106-8f71-4684-afc8-0309ddc4a3ca.dat" variableMetadata_out "/tmp/tmp77stj8bh/job_working_directory/000/23/outputs/dataset_513f093f-69b9-4ce5-b28c-f617f58e1d04.dat" information "/tmp/tmp77stj8bh/job_working_directory/000/23/outputs/dataset_ef200de1-84c1-4ec8-80f0-774d2bf09c57.dat"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
chromInfo	`"/tmp/tmp77stj8bh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
makeNameL	`"FALSE"`

Step 9: toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/5526f8258e8a/multivariate/multivariate_wrapper.R  dataMatrix_in "/tmp/tmp77stj8bh/files/d/7/d/dataset_d7da6ac8-70f7-440c-b148-48ccda4e1a00.dat" sampleMetadata_in "/tmp/tmp77stj8bh/files/e/0/2/dataset_e0266106-8f71-4684-afc8-0309ddc4a3ca.dat" variableMetadata_in "/tmp/tmp77stj8bh/files/5/1/3/dataset_513f093f-69b9-4ce5-b28c-f617f58e1d04.dat"  respC "none" predI "NA" orthoI "0" testL "FALSE"  typeC "summary" parAsColC "class" parCexN "0.8" parPc1I "1" parPc2I "2" parMahalC "NA" parLabVc "none"  algoC "default" crossvalI "3" log10L "FALSE" permI "20" scaleC "standard"  sampleMetadata_out "/tmp/tmp77stj8bh/job_working_directory/000/24/outputs/dataset_a197ff9d-1449-4c5f-8072-6c643f66eb08.dat" variableMetadata_out "/tmp/tmp77stj8bh/job_working_directory/000/24/outputs/dataset_30ab7b8e-5ce2-45dc-9ddc-8c6e9bbaf353.dat" figure "/tmp/tmp77stj8bh/job_working_directory/000/24/outputs/dataset_18063c80-16bf-4c0f-ac36-5bd5204ac156.dat" information "/tmp/tmp77stj8bh/job_working_directory/000/24/outputs/dataset_95bdb8d6-d66b-4ff0-b199-634caf69f538.dat"

Exit Code:

```
127
```

Standard Error:

Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6bb649fe7a7f11ef94c99b0a4a764b4f"`
advCpt	`{"__current_case__": 1, "algoC": "default", "crossvalI": "3", "log10L": "FALSE", "opcC": "full", "permI": "20", "scaleC": "standard"}`
advGph	`{"__current_case__": 1, "opgC": "full", "parAsColC": "class", "parCexN": "0.8", "parLabVc": "none", "parMahalC": "NA", "parPc1I": "1", "parPc2I": "2", "typeC": "summary"}`
chromInfo	`"/tmp/tmp77stj8bh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
orthoI	`"0"`
predI	`"NA"`
respC	`"none"`
save_rdata	`false`
testL	`"FALSE"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 7f8ec046ca48a6fa
- history_state
  - error
- invocation_id
  - 7f8ec046ca48a6fa
- invocation_state
  - scheduled
- workflow_id
  - 7f8ec046ca48a6fa

gxydevbot · 2025-02-10T05:11:08Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2025-02-10T05:29:44Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ Mass-spectrometry__GCMS-with-metaMS.ga_0

Problems:

Output with path /tmp/tmpxpm2nlua/dataMatrix.tsv__4aa3538d-8177-45fc-be37-ea60af5a4e59 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/metabomics/gcms-metams/test-data/metaMS.runGC_dataMatrix.tabular v. /tmp/tmpq0j1kkqgmetaMS.runGC_dataMatrix.tabular )
--- local_file
+++ history_data
@@ -1,19 +1,19 @@
 Name	alg11	alg2	alg3	alg7	alg8	alg9
-Unknown 1	171208192	19403078	51689436	196528995	111241302	180946294
+Unknown 1	171208192	19403078	51689436	198391471	111241302	180946294
 Unknown 2	85088688	1386827	4976677	10589259	8917809	11005200
 Unknown 3	75099028	5873408	16302374	56198912	40418507	47836465
-Unknown 4	73997431	2895358	8986693	23638072	18739515	64542302
+Unknown 4	73997431	3271105	8986693	23638072	18739515	64542302
 Unknown 5	49891456	0	0	57808911	34317665	36298101
 Unknown 6	46647944	0	0	64737554	47489338	44537215
-Unknown 7	39902198	860385	4363914	4717721	1450738	48186709
-Unknown 8	28189000	0	0	11992763	20790174	19217984
+Unknown 7	34567152	860385	4363914	4717721	1450738	40987747
+Unknown 8	28189000	0	0	11992762	20790174	19217984
 Unknown 9	25076752	0	0	9137481	19261173	18374954
 Unknown 10	21548640	147001	68652	0	7588721	33772365
 Unknown 11	19375952	0	0	6892322	14909830	13761534
 Unknown 12	14178558	0	0	641511	2206833	8574065
 Unknown 13	13866886	454935	2093751	2134194	0	5900383
 Unknown 14	11467026	28030267	55915933	0	0	5658858
-Unknown 15	9142884	452747	1213592	5440450	11763699	9759910
+Unknown 15	9142884	452747	1213592	5440450	11763698	9759910
 Unknown 16	7689193	353781	855345	0	1759539	5866687
 Unknown 17	6263489	0	0	13625540	8486545	3597172
 Unknown 18	5826631	0	0	0	810446	2272925
@@ -31,7 +31,7 @@
 Unknown 30	1081990	0	0	333776	754995	594591
 Unknown 31	912243	0	0	537871	471554	956720
 Unknown 32	2569379	0	0	2947028	3457418	0
-Unknown 33	669269	0	0	230182	477082	406381
+Unknown 33	669269	0	0	232558	477082	406381
 Unknown 34	509995	0	0	1345463	1436544	0
 Unknown 35	413495	0	0	225550	0	417419
 Unknown 36	279749	38785	107787	65314	0	276001
@@ -39,4 +39,4 @@
 Unknown 38	126812	0	0	58744	0	120821
 Unknown 39	88527	0	0	0	71387	48406
 Unknown 40	0	101114	250239	456049	488211	0

Workflow invocation details

Invocation Messages

Steps

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

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/tmpz61hya13/files/d/2/8/dataset_d28a64d9-da73-4893-abae-4f9e556ed78b.dat' singlefile_sampleName 'alg11.mzData'   ; 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/tmpz61hya13/files/d/2/8/dataset_d28a64d9-da73-4893-abae-4f9e556ed78b.dat
singlefile_sampleName	alg11.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
             sample_name sample_group
alg11.mzData       alg11            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
             sample_name sample_group
alg11.mzData       alg11            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/tmpz61hya13/files/0/8/1/dataset_08120d0c-bad2-4185-8232-1803c94bafc4.dat' singlefile_sampleName 'alg2.mzData'   ; 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/tmpz61hya13/files/0/8/1/dataset_08120d0c-bad2-4185-8232-1803c94bafc4.dat
singlefile_sampleName	alg2.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg2.mzData        alg2            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg2.mzData        alg2            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/tmpz61hya13/files/b/1/9/dataset_b19d2141-313d-4bbc-b676-fd86bf271f61.dat' singlefile_sampleName 'alg3.mzData'   ; 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/tmpz61hya13/files/b/1/9/dataset_b19d2141-313d-4bbc-b676-fd86bf271f61.dat
singlefile_sampleName	alg3.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg3.mzData        alg3            .
			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: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg3.mzData        alg3            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/tmpz61hya13/files/1/3/0/dataset_130c85a7-68ba-40bc-8484-7e7ebc4317e5.dat' singlefile_sampleName 'alg7.mzData'   ; 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/tmpz61hya13/files/1/3/0/dataset_130c85a7-68ba-40bc-8484-7e7ebc4317e5.dat
singlefile_sampleName	alg7.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg7.mzData        alg7            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg7.mzData        alg7            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/tmpz61hya13/files/8/a/1/dataset_8a133fe6-bf42-4648-a395-3c262388a323.dat' singlefile_sampleName 'alg8.mzData'   ; 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/tmpz61hya13/files/8/a/1/dataset_8a133fe6-bf42-4648-a395-3c262388a323.dat
singlefile_sampleName	alg8.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg8.mzData        alg8            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:34 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg8.mzData        alg8            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/tmpz61hya13/files/b/0/f/dataset_b0f3f2cf-ac87-4a36-95ea-66c286305f7a.dat' singlefile_sampleName 'alg9.mzData'   ; 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/tmpz61hya13/files/b/0/f/dataset_b0f3f2cf-ac87-4a36-95ea-66c286305f7a.dat
singlefile_sampleName	alg9.mzData


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
Compute md5 checksum...


	MAIN PROCESSING INFO
		COMPUTE
			Create a phenodata data.frame
            sample_name sample_group
alg9.mzData        alg9            .
			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: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:34 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
		phenoData
            sample_name sample_group
alg9.mzData        alg9            .


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"mzdata"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: 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/tmpz61hya13/files/0/4/0/dataset_040ba652-d4d9-4eec-ad8f-5e9c717ac622.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/0/4/0/dataset_040ba652-d4d9-4eec-ad8f-5e9c717ac622.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg11.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 3025 peaks identified in 1 samples.
 On average 3025 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1196.7 seconds (10-19.9 minutes)
Mass range: 50.9572-449.1296 m/z
Peaks: 3025 (about 3025 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.773 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

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/tmpz61hya13/files/4/3/7/dataset_43743611-95b8-4fac-8103-ba0c828172b6.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/4/3/7/dataset_43743611-95b8-4fac-8103-ba0c828172b6.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg2.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg2.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2268 peaks identified in 1 samples.
 On average 2268 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 600.8-1196.5 seconds (10-19.9 minutes)
Mass range: 50.2485-448.8367 m/z
Peaks: 2268 (about 2268 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.652 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

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/tmpz61hya13/files/a/b/6/dataset_ab68280e-ce0c-4af8-b51b-d0a5388b290b.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/a/b/6/dataset_ab68280e-ce0c-4af8-b51b-d0a5388b290b.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:57 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg3.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg3.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2576 peaks identified in 1 samples.
 On average 2576 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.8-1197.5 seconds (10-20 minutes)
Mass range: 50.1621-448.9793 m/z
Peaks: 2576 (about 2576 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.701 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

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/tmpz61hya13/files/0/4/6/dataset_04614de2-41c0-47d8-882d-da6c4a196c55.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/0/4/6/dataset_04614de2-41c0-47d8-882d-da6c4a196c55.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:20 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg7.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg7.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2466 peaks identified in 1 samples.
 On average 2466 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9493-449.2975 m/z
Peaks: 2466 (about 2466 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.684 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

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/tmpz61hya13/files/8/6/b/dataset_86b98fdb-239e-4b23-8ce6-eed13832d412.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/8/6/b/dataset_86b98fdb-239e-4b23-8ce6-eed13832d412.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:34 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg8.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg8.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2544 peaks identified in 1 samples.
 On average 2544 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 601.5-1197 seconds (10-20 minutes)
Mass range: 50.9637-449.1156 m/z
Peaks: 2544 (about 2544 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.696 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

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/tmpz61hya13/files/1/3/f/dataset_13f5d4c3-3fd0-4ead-82ca-15b1de4be1ce.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 5 binSize 0.5 impute none max 500 snthresh 2 steps 2 mzdiff 0.5 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c "exit $return"

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 4.0.5 (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/tmpz61hya13/files/1/3/f/dataset_13f5d4c3-3fd0-4ead-82ca-15b1de4be1ce.dat
BPPARAM	1
method	MatchedFilter
fwhm	5
binSize	0.5
impute	none
max	500
snthresh	2
steps	2
mzdiff	0.5
peaklist	FALSE


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE
			Apply filter[s] (if asked)
			Chromatographic peak detection
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
 impute: none 
 baseValue:  
 distance:  
 fwhm: 5 
 sigma: 2.123323 
 max: 500 
 snthresh: 2 
 steps: 2 
 mzdiff: 0.5 
 index: FALSE 
Creating the sampleMetadata file...
Error in R_nc4_open: NetCDF: Unknown file format


	XCMSnExp OBJECT INFO
MSn experiment data ("XCMSnExp")
Object size in memory: 0.63 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 1799 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Data loaded [Mon Feb 10 05:25:34 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg9.mzData
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  alg9.mzData 
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F1.S1799 (1799 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 2765 peaks identified in 1 samples.
 On average 2765 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
An "xcmsSet" object with 1 samples

Time range: 599.9-1197.7 seconds (10-20 minutes)
Mass range: 50.9528-448.9991 m/z
Peaks: 2765 (about 2765 per sample)
Peak Groups: 0 
Sample classes: . 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 0.732 MB


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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	`{"MatchedFilterAdv": {"impute_cond": {"__current_case__": 0, "impute": "none"}, "max": "500", "mzdiff": "0.5", "peaklist": false, "sigma": null, "snthresh": "2", "steps": "2"}, "__current_case__": 1, "binSize": "0.5", "fwhm": "5", "method": "MatchedFilter"}`

Step 5: 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/tmpz61hya13/files/a/d/2/dataset_ad2c4a3c-8c5e-440d-94bb-5f4567c4914f.dat","/tmp/tmpz61hya13/files/9/c/c/dataset_9ccecd5b-3d16-4d9a-80ff-0a4075711917.dat","/tmp/tmpz61hya13/files/6/e/d/dataset_6ed45bae-6e83-4b73-8f3d-bf0503949c5f.dat","/tmp/tmpz61hya13/files/b/2/6/dataset_b2649693-2efd-49fb-afa2-176fd1c55859.dat","/tmp/tmpz61hya13/files/3/6/b/dataset_36b7e338-c128-467c-b411-1e60013957f5.dat","/tmp/tmpz61hya13/files/c/5/b/dataset_c5b40994-f513-4c50-81b6-00ba6fb74ace.dat")'  sampleMetadata '/tmp/tmpz61hya13/files/5/2/8/dataset_528a06f2-77d2-4e2c-bb5a-1c4b4c863ba2.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	c("/tmp/tmpz61hya13/files/a/d/2/dataset_ad2c4a3c-8c5e-440d-94bb-5f4567c4914f.dat", "/tmp/tmpz61hya13/files/9/c/c/dataset_9ccecd5b-3d16-4d9a-80ff-0a4075711917.dat", "/tmp/tmpz61hya13/files/6/e/d/dataset_6ed45bae-6e83-4b73-8f3d-bf0503949c5f.dat", "/tmp/tmpz61hya13/files/b/2/6/dataset_b2649693-2efd-49fb-afa2-176fd1c55859.dat", "/tmp/tmpz61hya13/files/3/6/b/dataset_36b7e338-c128-467c-b411-1e60013957f5.dat", "/tmp/tmpz61hya13/files/c/5/b/dataset_c5b40994-f513-4c50-81b6-00ba6fb74ace.dat")
sampleMetadata	/tmp/tmpz61hya13/files/5/2/8/dataset_528a06f2-77d2-4e2c-bb5a-1c4b4c863ba2.dat


	ARGUMENTS PROCESSING INFO


	INFILE PROCESSING INFO
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Mon Feb 10 05:26:38 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	DONE

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_load_section	`{"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}`

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/tmpz61hya13/files/a/d/2/dataset_ad2c4a3c-8c5e-440d-94bb-5f4567c4914f.dat","/tmp/tmpz61hya13/files/9/c/c/dataset_9ccecd5b-3d16-4d9a-80ff-0a4075711917.dat","/tmp/tmpz61hya13/files/6/e/d/dataset_6ed45bae-6e83-4b73-8f3d-bf0503949c5f.dat","/tmp/tmpz61hya13/files/b/2/6/dataset_b2649693-2efd-49fb-afa2-176fd1c55859.dat","/tmp/tmpz61hya13/files/3/6/b/dataset_36b7e338-c128-467c-b411-1e60013957f5.dat","/tmp/tmpz61hya13/files/c/5/b/dataset_c5b40994-f513-4c50-81b6-00ba6fb74ace.dat")'  sampleMetadata '/tmp/tmpz61hya13/files/5/2/8/dataset_528a06f2-77d2-4e2c-bb5a-1c4b4c863ba2.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...
alg11 
alg2 
alg3 
alg7 
alg8 
alg9 
	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


	XCMSnExp OBJECT INFO
             sample_name   sample_group
alg11.mzData       alg11 FWS_100perNaCl
alg2.mzData         alg2            SWS
alg3.mzData         alg3            SWS
alg7.mzData         alg7  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl
MSn experiment data ("XCMSnExp")
Object size in memory: 3.1 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 10794 
 MSn retention times: 9:60 - 19:58 minutes
- - - Processing information - - -
Concatenated [Mon Feb 10 05:26:38 2025] 
 MSnbase version: 2.16.1 
- - - Meta data  - - -
phenoData
  rowNames: alg11.mzData alg2.mzData ... alg9.mzData (6 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] alg11.mzData...  [6] alg9.mzData
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F6.S1799 (10794 total)
  fvarLabels: fileIdx spIdx ... spectrum (35 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: matchedFilter 
 15644 peaks identified in 6 samples.
 On average 2607 chromatographic peaks per sample.


	xcmsSet OBJECT INFO
             sample_name   sample_group          class
alg11.mzData       alg11 FWS_100perNaCl FWS_100perNaCl
alg2.mzData         alg2            SWS            SWS
alg3.mzData         alg3            SWS            SWS
alg7.mzData         alg7  FWS_5percNaCL  FWS_5percNaCL
alg8.mzData         alg8  FWS_5percNaCL  FWS_5percNaCL
alg9.mzData         alg9 FWS_100perNaCl FWS_100perNaCl
An "xcmsSet" object with 6 samples

Time range: 599.8-1197.7 seconds (10-20 minutes)
Mass range: 50.1621-449.2975 m/z
Peaks: 15644 (about 2607 per sample)
Peak Groups: 0 
Sample classes: FWS_100perNaCl, SWS, FWS_5percNaCL 

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1799 
Profile settings: method = bin
                  step = 0.1

Memory usage: 4.2 MB


	SAVE RData

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/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/yguitton/metams_rungc/metams_runGC/3.0.0+metaMS1.24.0-galaxy0:

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/yguitton/metams_rungc/93508ea69eb5/metams_rungc///metaMS_runGC.r  singlefile_galaxyPath '/tmp/tmpz61hya13/files/b/7/6/dataset_b764c14f-04a9-43a3-b2da-766b2593badd.dat' singlefile_sampleName 'xset.merged.RData'  settings "User_defined" rtdiff 0.05 minfeat 5 simthreshold 0.7 minclassfraction 0.5 minclasssize 3 rtrange "NULL" ri "NULL" rishift "none" db "NULL" nSlaves ${GALAXY_SLOTS:-1}

Exit Code:

```
0
```

Standard Error:

Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
< -------- Experiment of 6 samples ------------------------------------- >
< -------- Instrument: GALAXY.GC --------------------------------------- >
< -------- No annotation performed ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >

Standard Output:

	SESSION INFO

R version 4.0.5 (2021-03-31) 
Main packages:
batch 1.1.5 	stringr 1.4.1 	metaMS 1.24.0 	CAMERA 1.44.0 	xcms 3.10.0 	MSnbase 2.14.1 	ProtGenerics 1.20.0 	S4Vectors 0.26.0 	mzR 2.22.0 	Rcpp 1.0.9 	BiocParallel 1.22.0 	Biobase 2.48.0 	BiocGenerics 0.34.0 	
Other loaded packages:
bitops 1.0.7 	matrixStats 0.62.0 	doParallel 1.0.17 	RColorBrewer 1.1.3 	GenomeInfoDb 1.24.0 	tools 4.0.5 	backports 1.4.1 	utf8 1.2.2 	R6 2.5.1 	affyio 1.58.0 	rpart 4.1.16 	Hmisc 4.7.1 	colorspace 2.0.3 	nnet 7.3.17 	gridExtra 2.3 	compiler 4.0.5 	MassSpecWavelet 1.54.0 	preprocessCore 1.50.0 	graph 1.66.0 	cli 3.4.1 	htmlTable 2.4.1 	DelayedArray 0.14.0 	scales 1.2.1 	checkmate 2.1.0 	DEoptimR 1.0.11 	robustbase 0.95.0 	affy 1.66.0 	RBGL 1.64.0 	digest 0.6.29 	foreign 0.8.82 	XVector 0.28.0 	base64enc 0.1.3 	jpeg 0.1.9 	pkgconfig 2.0.3 	htmltools 0.5.3 	fastmap 1.1.0 	limma 3.44.1 	htmlwidgets 1.5.4 	rlang 1.0.6 	rstudioapi 0.14 	impute 1.62.0 	mzID 1.26.0 	RCurl 1.98.1.8 	magrittr 2.0.3 	GenomeInfoDbData 1.2.4 	Formula 1.2.4 	interp 1.1.3 	MALDIquant 1.21 	Matrix 1.4.1 	munsell 0.5.0 	fansi 1.0.3 	lifecycle 1.0.2 	vsn 3.56.0 	stringi 1.7.8 	MASS 7.3.58.1 	SummarizedExperiment 1.18.1 	zlibbioc 1.34.0 	plyr 1.8.7 	grid 4.0.5 	deldir 1.0.6 	lattice 0.20.45 	splines 4.0.5 	knitr 1.40 	pillar 1.8.1 	igraph 1.3.1 	GenomicRanges 1.40.0 	codetools 0.2.18 	XML 3.99.0.10 	glue 1.6.2 	latticeExtra 0.6.30 	pcaMethods 1.80.0 	data.table 1.14.2 	BiocManager 1.30.18 	png 0.1.7 	vctrs 0.4.1 	foreach 1.5.2 	gtable 0.3.1 	RANN 2.6.1 	ggplot2 3.3.6 	xfun 0.33 	ncdf4 1.19 	survival 3.4.0 	tibble 3.1.8 	iterators 1.0.14 	IRanges 2.22.1 	cluster 2.1.3 	



Start of the 'metaMS:runGC' Galaxy module call: Mon 10 Feb 2025 05:27:44


	ARGUMENTS PROCESSING INFO

                      value                                                                          
singlefile_galaxyPath "/tmp/tmpz61hya13/files/b/7/6/dataset_b764c14f-04a9-43a3-b2da-766b2593badd.dat"
singlefile_sampleName "xset.merged.RData"                                                            
settings              "User_defined"                                                                 
rtdiff                "0.05"                                                                         
minfeat               "5"                                                                            
simthreshold          "0.7"                                                                          
minclassfraction      "0.5"                                                                          
minclasssize          "3"                                                                            
rtrange               "NULL"                                                                         
ri                    "NULL"                                                                         
rishift               "none"                                                                         
db                    "NULL"                                                                         
nSlaves               "1"                                                                            


	ARGUMENTS PROCESSING INFO

Using user's parameters
rtrange= 


	INFILE PROCESSING INFO


	MAIN PROCESSING INFO
		COMPUTE

Loading datas from XCMS files...
Process xsAnnotate with CAMERA package...
Process runGC with metaMS package...

Formal class 'metaMSsettings' [package "metaMS"] with 30 slots
  ..@ protocolName                      : chr "GALAXY.GC"
  ..@ chrom                             : chr "GC"
  ..@ PeakPicking                       :List of 7
  .. ..$ method  : chr "matchedFilter"
  .. ..$ step    : num 0.5
  .. ..$ steps   : num 2
  .. ..$ mzdiff  : num 0.5
  .. ..$ fwhm    : num 5
  .. ..$ snthresh: num 2
  .. ..$ max     : num 500
  ..@ Alignment                         : list()
  ..@ CAMERA                            :List of 1
  .. ..$ perfwhm: num 1
  ..@ match2DB.rtdiff                   : num 0.05
  ..@ match2DB.minfeat                  : num 5
  ..@ match2DB.rtval                    : num(0) 
  ..@ match2DB.mzdiff                   : num(0) 
  ..@ match2DB.ppm                      : num(0) 
  ..@ match2DB.simthresh                : num 0.7
  ..@ match2DB.timeComparison           : chr "rt"
  ..@ match2DB.RIdiff                   : num 5
  ..@ DBconstruction.minfeat            : num 5
  ..@ DBconstruction.rttol              : num 0.05
  ..@ DBconstruction.mztol              : num(0) 
  ..@ DBconstruction.minintens          : num 0
  ..@ DBconstruction.intensityMeasure   : chr "maxo"
  ..@ DBconstruction.DBthreshold        : num 0.8
  ..@ matchIrrelevants.irrelevantClasses: chr(0) 
  ..@ matchIrrelevants.simthresh        : num(0) 
  ..@ matchIrrelevants.timeComparison   : chr(0) 
  ..@ matchIrrelevants.RIdiff           : num(0) 
  ..@ matchIrrelevants.rtdiff           : num(0) 
  ..@ betweenSamples.min.class.fraction : num 0.5
  ..@ betweenSamples.min.class.size     : num 3
  ..@ betweenSamples.timeComparison     : chr "rt"
  ..@ betweenSamples.rtdiff             : num 0.05
  ..@ betweenSamples.RIdiff             : num 2
  ..@ betweenSamples.simthresh          : num 0.7
NULL

Generating peakTable file	.	.	.	OK
Generating dataMatrix file	.	.	.	OK
Generating variableMetadata file	.	.	OK
Generating sampleMetadata file	.	.	.	OK
Generating 41 peakspectra in peakspectra.msp file

End of 'metaMS:runGC' Galaxy module call: 2025-02-10 05:27:47

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"rdata.xcms.findchrompeaks"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
options_rifilter	`{"__current_case__": 1, "option": "false"}`
settings	`{"__current_case__": 1, "minclassfraction": "0.5", "minclasssize": "3", "minfeat": "5", "options_db": {"__current_case__": 1, "option": "hide"}, "options_ri": {"__current_case__": 1, "option": "hide"}, "options_rtrange": {"__current_case__": 1, "option": "hide"}, "rtdiff": "0.05", "setting": "usersettings", "simthreshold": "0.7"}`

Step 8: 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/tmpz61hya13/files/4/a/a/dataset_4aa3538d-8177-45fc-be37-ea60af5a4e59.dat" sampleMetadata_in "/tmp/tmpz61hya13/files/5/2/8/dataset_528a06f2-77d2-4e2c-bb5a-1c4b4c863ba2.dat" variableMetadata_in "/tmp/tmpz61hya13/files/2/e/7/dataset_2e7a6f6d-7095-42a1-beb6-3918470c042b.dat" makeNameL "FALSE"  dataMatrix_out "/tmp/tmpz61hya13/job_working_directory/000/23/outputs/dataset_a1c55c96-dfcf-4d1e-987a-2409fcee5f52.dat" sampleMetadata_out "/tmp/tmpz61hya13/job_working_directory/000/23/outputs/dataset_4741b640-cc1e-48a3-a0df-370b802d860f.dat" variableMetadata_out "/tmp/tmpz61hya13/job_working_directory/000/23/outputs/dataset_1b4606ef-ec14-4107-960b-d383fd3da742.dat" information "/tmp/tmpz61hya13/job_working_directory/000/23/outputs/dataset_67886cb0-7d8c-4d38-a189-9b499c27e30d.dat"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
chromInfo	`"/tmp/tmpz61hya13/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
makeNameL	`"FALSE"`

Step 9: toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/5526f8258e8a/multivariate/multivariate_wrapper.R  dataMatrix_in "/tmp/tmpz61hya13/files/a/1/c/dataset_a1c55c96-dfcf-4d1e-987a-2409fcee5f52.dat" sampleMetadata_in "/tmp/tmpz61hya13/files/4/7/4/dataset_4741b640-cc1e-48a3-a0df-370b802d860f.dat" variableMetadata_in "/tmp/tmpz61hya13/files/1/b/4/dataset_1b4606ef-ec14-4107-960b-d383fd3da742.dat"  respC "none" predI "NA" orthoI "0" testL "FALSE"  typeC "summary" parAsColC "class" parCexN "0.8" parPc1I "1" parPc2I "2" parMahalC "NA" parLabVc "none"  algoC "default" crossvalI "3" log10L "FALSE" permI "20" scaleC "standard"  sampleMetadata_out "/tmp/tmpz61hya13/job_working_directory/000/24/outputs/dataset_ce6d48bc-020e-43dd-b9ac-8b72d1a2f1ce.dat" variableMetadata_out "/tmp/tmpz61hya13/job_working_directory/000/24/outputs/dataset_f61c3152-6f91-4be5-8b11-8f872202d51b.dat" figure "/tmp/tmpz61hya13/job_working_directory/000/24/outputs/dataset_234e1760-20d7-413d-96f9-5f533210ed1a.dat" information "/tmp/tmpz61hya13/job_working_directory/000/24/outputs/dataset_3e944c12-de2f-46c4-b6d1-e65fed3a9a8b.dat"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"533e17c8e76f11efb46f6045bd7e34d9"`
advCpt	`{"__current_case__": 1, "algoC": "default", "crossvalI": "3", "log10L": "FALSE", "opcC": "full", "permI": "20", "scaleC": "standard"}`
advGph	`{"__current_case__": 1, "opgC": "full", "parAsColC": "class", "parCexN": "0.8", "parLabVc": "none", "parMahalC": "NA", "parPc1I": "1", "parPc2I": "2", "typeC": "summary"}`
chromInfo	`"/tmp/tmpz61hya13/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
orthoI	`"0"`
predI	`"NA"`
respC	`"none"`
save_rdata	`false`
testL	`"FALSE"`

Other invocation details
- history_id
  - 7bab49a4488695aa
- history_state
  - ok
- invocation_id
  - 7bab49a4488695aa
- invocation_state
  - scheduled
- workflow_id
  - 7bab49a4488695aa

gxydevbot changed the title ~~Updating workflows/metabomics/gcms-metams from 0.1 to 0.2~~ Updating workflows/metabomics/gcms-metams from 0.1 to 0.2 Sep 23, 2024

gxydevbot force-pushed the workflows/metabomics/gcms-metams branch from e4aefac to 6c8ac02 Compare September 23, 2024 14:30

gxydevbot force-pushed the workflows/metabomics/gcms-metams branch from 6c8ac02 to 4c09ffd Compare September 24, 2024 14:07

Updating workflows/metabomics/gcms-metams from 0.1 to 0.2

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gxydevbot force-pushed the workflows/metabomics/gcms-metams branch from 4c09ffd to 8d96b28 Compare February 10, 2025 05:11

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Updating workflows/metabomics/gcms-metams from 0.1 to 0.2 #303

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