I am following a tutorial from openms which involves a workflow using OMSSA in KNIME. Upon inputting my own work files and Uniprot database, I get the following error. It seems that KNIME is unable to find the executable file. I suspected it might be caused by the space in the KNIME application name (originally /Applications/KNIME 4.1.0.app/…). However, after changing to “/Applications/KNIME-4.1.0.app/…”, the problem still persists.
ERROR OMSSAAdapter 0:9 Failing process stdout: [Warning: unable to determine the version of OMSSA - the process returned an error. Call string was: ‘/Applications/KNIME-4.1.0.app/Contents/Eclipse/plugins/de.openms.macosx.x86_64_2.6.0.202004161737/payload/bin/OMSSA/omssacl -version’. Make sure that the OMSSA executable given in ‘-omssa_executable’ is correct!, OMSSAAdapter took 0.01 s (wall), 0.01 s (CPU), 0.00 s (system), 0.01 s (user).]
ERROR OMSSAAdapter 0:9 Failing process stderr:
ERROR OMSSAAdapter 0:9 Return code: 6
ERROR OMSSAAdapter 0:9 Execute failed: Failed to execute node OMSSAAdapter
Anyone encounter the same issue and knows the solution?
Did you check manually if the executable is at the place it is trying to look for? Call string was: ‘/Applications/KNIME-4.1.0.app/Contents/Eclipse/plugins/de.openms.macosx.x86_64_2.6.0.202004161737/payload/bin/OMSSA/omssacl
If it is there, can you try to open a command line there and execute it to see if it is executable?
Actually I can confirm on macOS Catalina. Unfortunately Apple dropped 32bit support
since Catalina. We will try to rebuild OMSSA but since it is to my knowledge not really maintained anymore, I cannot promise anything.
Until then (and also for future-proof pipelines) I would suggest to move to a newer search engine like Comet or MSGFPlus.
Certainly, we have to update the tutorials on our side.
You can follow the progress on this issue here: https://github.com/OpenMS/OpenMS/issues/4281