File Converter does not work

[luizimgiolo]

Hi there, I'm trying to run the workflow of Optmus on Knime, but I'm stucked on the following issue. On the Step 2: data analysis, I get the error at console:

> 'ERROR FileConverter 0:423:325:277 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:290 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:298 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:277 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:322 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:306 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:282 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:302:314 Execute failed: The tool executor 'com.genericworkflownodes.knime.execution.impl.LocalToolExecutor' is not known. Please check your configuration. > ERROR FileConverter 0:423:325:277 Errors found loading Settings from disk. Maybe you are loading a node created with another version. > Using default values as defined in the Tool description. > We recommend to check the parameters highlighted in red carefully before clicking OK: > - Entry for FileConverter.1.force_MaxQuant_compatibility not found in settings.xml. > - Entry for FileConverter.1.force_TPP_compatibility not found in settings.xml. > - Entry for FileConverter.1.write_scan_index not found in settings.xml. > - Entry for FileConverter.1.lossy_compression not found in settings.xml. > - Entry for FileConverter.1.lossy_mass_accuracy not found in settings.xml. > looking through the "Detect LC-MS features" node, the "X" is at FileConverter and inside FileConverter the red lines are: - force_MaxQuant_compatibility - force_TPP_compatibility - write_scan_index - lossy_copression - lossy_mass_accuracy If someone have any solution I'll apreciate appreciate

[iprotsyuk]

Hi @luizimgiolo, sorry for the delay with response. It seems that the FileConverter tool was updated recently by OpenMS team s.t. its settings are incompatible with the previous version, but your KNIME downloaded this update automatically and became incompatible with Optimus. The only thing I can suggest here is to download a previous KNIME version v3.3.1 (make sure to download the version with all extensions included) from this page https://www.knime.com/download-previous-versions , make sure to ignore KNIME notifications about new updates and try to run Optimus with it. Let me know if it works for you

[luizimgiolo]

I've tryed this either, but the earlier version of OpenMS available is 2.1.0, and the flow claims that 2.0.0 is necessary. I'm testing with some mzML files and finding another bugs because of the recent OpenMS update. Example: Inside metanode 'Detect LC-MS features', we have the another metanode 'Detect LC-MS features', and inside that the node 'FeatureFinderMetabo' never works, but if we replace for the same node from the new version, the flow works nicely. I'll try others replacements like that next week, after that I'll update the comment.

Thak you for the answer

[iprotsyuk]

Alright, I didn’t realize how much you are proficient with knime :) what I’d suggest in this case is to replace OpenMS nodes producing errors in Optimus with same nodes, but created inside your version of knime by drag&drop from the knime node collection to the workflow scene. Try to use the same settings in new nodes as in the original ones. You should see that the new nodes have slightly different configurations compared to the previous versions: some parameters may be missing, or new ones are added. Connect new new nodes to the same inputs and outputs as original ones and delete the latter ones. I’d recommend doing this one-node-at-a-time to replace only those nodes that are indeed incompatible

[luizimgiolo]

I'm just a beginner with knime, but I'm reading the tutorial that OpenMS made. My next week goals will be try to update the nodes.

Thaks for all the inputs

[iprotsyuk]

Hi @luizimgiolo, I'm closing the issue for now. Feel free to reopen it or create a new one if you continue experiencing issues

[luizimgiolo]

Hey Ivan, Thanks for all the help. I was on vacation, so I did not solved the problem yet. I'll keep trying, if I have any success I'll post it, but for now our group is keeping the focus on mzMine.

On Mon, Jun 11, 2018 at 6:44 PM, Ivan Protsyuk notifications@github.com wrote:

Closed #8 https://github.com/MolecularCartography/Optimus/issues/8.

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