MapAlignerPoseClustering and FeatureLinkerUnlabeledQT errors


Hi All,

I’m new to using both Knime (v 4.0.0) and OpenMS on metabolomics data processing and I’m having a hard time getting past the MapAlignerPoseClustering and FeatureLinkerUnlabeledQT steps. I’ve tried to follow this workflow from tutorial section 5 exactly, but it leads to errors on the aforementioned steps.

Some details: I’m using a Windows virtual machine and using as many as 10 .mzML files obtained through centroiding with ProteoWizard.
The steps from input -> ziploopEnd seem to execute without any issues.

For MapAlignerPoseClustering, I get this error:

ERROR MapAlignerPoseClustering 2:5 Failing process stdout: [Picking a reference (by size) … done, Progress of ‘Aligning input maps’:, FeatureXMLFile::store(): found 1 invalid unique ids, , ---------------------------------------------------, FATAL: uncaught exception!, ---------------------------------------------------, last entry in the exception handler: , exception of type IllegalArgument occured in line 742, function void __cdecl OpenMS::PoseClusteringAffineSuperimposer::run(const class std::vector<class OpenMS::Peak2D,class std::allocator > &,const class std::vector<class OpenMS::Peak2D,class std::allocator > &,class OpenMS::TransformationDescription &) of C:\jenkins\ws\openms_release_packaging\c2e226b2\source\src\openms\source\ANALYSIS\MAPMATCHING\PoseClusteringAffineSuperimposer.cpp, error message: One of the input maps is empty! This is not allowed!, ---------------------------------------------------]
ERROR MapAlignerPoseClustering 2:5 Failing process stderr:
ERROR MapAlignerPoseClustering 2:5 Execute failed: Failed to execute node MapAlignerPoseClustering

For the FeatureLinkerUnlabeledQT step, my error message is:

ERROR FeatureLinkerUnlabeledQT 2:6 Failing process stdout: [Linking 2 featureXMLs., Progress of ‘reading input’:, , – done [took 0.00 s (CPU), 0.00 s (Wall)] – ]
ERROR FeatureLinkerUnlabeledQT 2:6 Failing process stderr:
ERROR FeatureLinkerUnlabeledQT 2:6 Execute failed: Failed to execute node FeatureLinkerUnlabeledQT

What can be going wrong? Is my feature finding not yielding any output?




Indeed that might be the case for at least one of your inputs.
You can check the standard output of the previous FeatureFinder by right-clicking
on it and selecting “View: Standard Output”.
It hopefully complains about something during feature finding.



Hi jpfeuffer,

This is what the “Standard Output” looks like below. It’s telling me that there is an “unknown parameter ‘noise_threshold_int’”. Kind of confusing seeing how this is a supplied parameter to the FeatureFinder.

I changed its value a few times- 1000, 10, 5- but still the same result.

Also this message, “found 1 invalid unique ids”… I don’t know what the deal with that is.

I’ve tried different combinations of files and the result is always the same. These .mzML files run fine with other preprocessing programs like XCMS & MZMine2, so I don’t think the files themselves are the problem.



If it helps at all, I’ve attached the images of these parameter sets. Do you see parameter here that could lead to these errors?



Thanks for all the information. But let’s continue the discussion on the OpenMS GitHub since it turned out to be about the tool(s) itself :wink: