force: Overrides tool-specific checks

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1

I don’t why but my FeatureFinderCentroided didn’t execute. Just erros as “Execute failed: Failed to execute node FeatureFinderCentroided”. Is it related with my input files? But if I checked force: Overrides tool-specific checks as true. The workflow can execute. I don’t understand exactly what it means “Overrides tool-specific checks” but will it affect the true outputs?
Thanks!

2

Hi!

There should be a more complete log on the KNIME console or when you right-click the node and click on “View -> $Node Std Output” or “View -> $Node Std Error”.
Can you post this here?

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Hi Thanks for the reply! Below is the error. Sorry I’m new to OpenMS. I did provide centroided data.

ERROR FeatureFinderCentroided 0:4 Failing process stdout: [Warning: Parameters file version (2.6.0-pre-nightly-2020-12-13) does not match the version of this tool (2.6.0)., Your current parameters are still valid, but there might be new valid values or even new parameters. Upgrading the INI might be useful., Progress of ‘loading spectra list’:, , 1.69 % , 3.38 % , 5.08 % , 8.36 % , 10.15 % , 11.84 % , 14.94 % , 16.92 % , 18.61 % , 20.76 % , 22.71 % , 23.69 % , 25.38 % , 26.62 % , 27.78 % , 30.12 % , 32.15 % , 34.72 % , 37.23 % , 38.92 % , 42.30 % , 45.69 % , 50.14 % , 52.45 % , 55.84 % , 57.53 % , 58.93 % , 59.39 % , 61.44 % , 64.16 % , 64.99 % , 67.16 % , 68.65 % , 70.12 % , 72.12 % , 74.45 % , 76.14 % , 77.83 % , 79.53 % , 80.73 % , 81.22 % , 82.91 % , 84.52 % , 84.74 % , 86.29 % , 86.73 % , 87.99 % , 89.80 % , 93.33 % , 98.14 % , 98.75 % , – done [took 19.86 s (CPU), 51.30 s (Wall)] – , Progress of ‘loading chromatogram list’:, , – done [took 0.00 s (CPU), 0.03 s (Wall)] – , Error: Unexpected internal error (Error: Profile data provided but centroided spectra expected. To enforce processing of the data set the -force flag.)]
ERROR FeatureFinderCentroided 0:4 Failing process stderr:
ERROR FeatureFinderCentroided 0:4 Return code: 8
ERROR FeatureFinderCentroided 0:4 Execute failed: Failed to execute node FeatureFinderCentroided

4

Hi,

The problem is that many converters do not correctly label all the spectra as centroided although they centroid them. You will have to look inside the mzMLs to check that.

Either report the problem to the conversion software or do the peakpicking with the PeakPickerHiRes node.

EDIT: the --force flag might be OK in this case (if you are completely sure that everything is correctly peak picked).

Best
Julianus

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