collector node?

[villar]

Dear all,

I'm trying to get openMS working under KNIME  2.11.3 (the computer runs under windows 7, 64 bits). I'm particularly interested on performing alignment of LC-MS runs. I downloaded the pipeline referred in Aiche et al. Proteomics 2015 (wrokflow 2, label-free quantification of metabolites). I also donwloaded the corresponding input files, corrected the node "input files" (so that now KNIME has the right paths to the LC-MS data), and started. However, I get problems with MapAlignerPoseClustering and FeatureLinkerUnlabeledQT.

ERROR     FeatureFinderMetabo                Loading model settings failed: String for key "FeatureFinderMetabo.1.force" not found.
ERROR     MapAlignerPoseClustering           Loading model settings failed: String for key "MapAlignerPoseClustering.1.force" not found.
WARN      FeatureLinkerUnlabeledQT           Invalid MIMEtype at port number 0 : has extension: [application/x-mzml]; expected on of:[[featurexml, consensusxml]]
ERROR     LoadWorkflowRunnable               Errors during load: Status: Error: Example2_Metabolite_ID_Workflow 3 loaded with errors
ERROR     LoadWorkflowRunnable                 Status: Error: Example2_Metabolite_ID_Workflow 3
ERROR     LoadWorkflowRunnable                   Status: Error: FeatureFinderMetabo 3:106
ERROR     LoadWorkflowRunnable                     Status: Error: Loading model settings failed: String for key "FeatureFinderMetabo.1.force" not found.
ERROR     LoadWorkflowRunnable                   Status: Error: MapAlignerPoseClustering 3:29
ERROR     LoadWorkflowRunnable                     Status: Error: Loading model settings failed: String for key "MapAlignerPoseClustering.1.force" not found.

To debug, I truncated the pipeline, deleting all the nodes after FeatureLinkerUnlabeledQT and placing a generic Output Folder node after it:

InputFiles->ZipLoopStart->FeatureFinderMetabo->ZipLoopEnd->MapAlignerPoseClustering->FeatureLinkerUnlabeledQT->OutputFolder

If I try to run it again, FeatureFinderMetabo works and the pipeline stucks after MapAlignerPoseClustering; all the nodes are green except for FeatureLinkerUnlabeledQT and OutputFiles, which are marked red. The log message is:

WARN      FeatureLinkerUnlabeledQT           Invalid MIMEtype at port number 0 : has extension: [application/x-mzml]; expected on of:[[featurexml, consensusxml]]
WARN      FeatureLinkerUnlabeledQT           Invalid MIMEtype at port number 0 : has extension: [application/x-mzml]; expected on of:[[featurexml, consensusxml]]
WARN      FeatureLinkerUnlabeledQT           Invalid MIMEtype at port number 0 : has extension: [application/x-mzml]; expected on of:[[featurexml, consensusxml]]

I don't know if the following small trouble I got with standalone OpenMS 1.12 and 2.0 (win 7, 64 bits) is somehow related to this or if this can help with the troubleshooting. In standalone OpenMS  I could only get MapAlignerPoseClustering and FeatureLinkerUnlabeledQT working properly in similar pipelines if I placed a Collector node immediately before MapAlignerPoseClustering. I don' t find such a Collector node under KNIME.

 If you need more details or files, please let me know.

Best wishes

Ana

[jpfeuffer]

Hello Ana,

I hope that you can still use this answer, otherwise I will put it here for other people:

1)

ERROR     FeatureFinderMetabo                
Loading model settings failed: String for key "FeatureFinderMetabo.1.force" not found.

Indicates that the version of the node that you imported with the downloaded workflow does not match the version of the nodes that you currently have installed in KNIME (one configurable parameter called "force", was removed here). However, this usually can be solved by replacing these nodes with a fresh node with the same name from your current repository of nodes. (It seems you finally did it that way).

2)

WARN      FeatureLinkerUnlabeledQT
Invalid MIMEtype at port number 0 : 
has extension: [application/x-mzml]; 
expected one of:[[featurexml, consensusxml]]

tells you that the MIMEType (like file type/extension) that is going into a successor node is not correct. I suspect you forgot to set the correct OutputTypes in the second tab of the Configure dialog of the predecessor (i.e. MapAlignerPoseClustering; from mzML to featureXML).

We are currently thinking about a more convenient versioning system of our nodes.

Best wishes,

Julianus