Error: findFeatures(..., 'openms')

[diasmandala]

Hello,

When i created newproject(), the script was generated automatically. However, when i run findfeatures(...,'openms')

this error came:

0% Error in errorHandler(cmd = commandQueue[[ci]], exitStatus = exitStatus, : Failed to run command 'C:/Program Files/OpenMS-2.3.0/bin/FeatureFinderMetabo.exe' with args: '-algorithm:common:noise_threshold_int 1000 -algorithm:common:chrom_fwhm 5 -algorithm:mtd:mass_error_ppm 10 -algorithm:mtd:trace_termination_criterion sample_rate -algorithm:mtd:min_trace_length 3 -algorithm:mtd:max_trace_length -1 -algorithm:epd:width_filtering fixed -algorithm:epd:min_fwhm 3 -algorithm:epd:max_fwhm 60 -algorithm:ffm:report_convex_hulls true -in C:/~/tiny4_LTQ-FT.mzML0.99.0.mzML -out C:\~\AppData\Local\Temp\RtmpcFSN1B\tiny4_LTQ-FT.mzML0.99.029ec5cd575ec.featureXML'. Exit code: 3

Anyway, I used analyse .mzml data. I did not use DataAnalysis Method in setup.

Thank you in advance,

Regards,

[rickhelmus]

Hello,

Can you check the logs OpenMS generated? Can you also share the processing script that was generated?

[yguitton]

Hi,

I think I have quite the same issue see error and code below. NOTE the commande line launched in cmd is working and creates the *.featureXML file. But I didn't managed to load it back into fList object manually.

CODE and Error

library(patRoon) dataDir <- patRoonData::exampleDataPath() # path to example data files generateAnalysisInfo(dataDir)

anaInfo <- generateAnalysisInfo(dataDir, groups = c(rep("solvent", 3), rep("standard", 3)), refs = "solvent")

anaInfo

options("patRoon.path.OpenMS" = "C:/Users/ygu/Documents/PCPOR066_YGU/!BioInformatics/PFCA_Codes/R_dev/PatRoon/OpenMS-2.3.0/bin")

BUG HERE

fList <- findFeatures(anaInfo, "openms", mzppm = 5)

Finding features with OpenMS for 6 analyses ... | | 0%Error in errorHandler(cmd = commandQueue[[ci]], exitStatus = exitStatus, : Failed to run command 'C:/Users/ygu/Documents/PCPOR066_YGU/!BioInformatics/PFCA_Codes/R_dev/PatRoon/OpenMS-2.3.0/bin/FeatureFinderMetabo.exe' with args: '-algorithm:common:noise_threshold_int 1000 -algorithm:common:chrom_fwhm 5 -algorithm:mtd:mass_error_ppm 5 -algorithm:mtd:trace_termination_criterion sample_rate -algorithm:mtd:min_trace_length 3 -algorithm:mtd:max_trace_length -1 -algorithm:epd:width_filtering fixed -algorithm:epd:min_fwhm 3 -algorithm:epd:max_fwhm 60 -algorithm:ffm:report_convex_hulls true -in C:/PFCA/YGU/PatRoon/R-Portable/App/R-Portable/library/patRoonData/extdata/solvent-1.mzML -out C:\Users\ygu\AppData\Local\Temp\RStudioPortableTemp\RtmpUnOQmW\solvent-122a43efa5e36.featureXML'. Exit code: 1

Cheers

[rickhelmus]

Hello,

Thanks for the feedback. Quite interesting you can run the command manually. Can you maybe try to run the command in R manually as well (e.g. with system2())?

Also, am I correct that you have an exclamation mark ('!') in your path to OpenMS? Perhaps some special characters are a problem at the moment.

[rickhelmus]

Closing due to inactivity.