I was doing RNAseq analysis and trying to re-run some of the samples that has previously failed alignment however when running the workflow I got this error Uncaught exception in exposed API method. Since then, I can’t even open any other tool and get the same error in everything. My history was large around 800Gb so I deleted items to reduce history size to 300Gb but it didn’t help. If I switch to other history, I can get the start page of the workflow or tool to load however if I start anything I get the same error or internal server error. I have tried different datasets (including those who were already successfully analyzed previously), different tools and different histories and still the error is persisting. Could someone please help?
It can sometimes mean that a workflow was corrupted when it is first uploaded to Galaxy. Loading it again can be a solution but not always.
Another solution can be to open the workflow in the editor and to review any messages in that first pop-up window – these are usually about tool versions that need to be updated. Galaxy will attempt to do this for you but try to keep track of those tools so you can review the parameters (these sometimes change across versions, in particular, any default settings you may have used).
While in the editor, you also may notice missing “Inputs” at the start or other disconnected tools. Resetting the workflow metadata by disconnected all noodles, then reconnecting in the order of tool execution, can be a way to resolve this situation.
Example: changing from a single input to a collection input can lead to a case where a downstream tool needs a different parameter set (example: to run in batch, or to merge together the outputs). Reconnecting the noodles can fix conflicts that may come up when trying to run the workflow without resetting the metadata for a collection first.
Please give those a try and let us know how it turns out! If you need more help, I would be curious about which Galaxy server you are working on, how this workflow was created, or where it was sourced (?), when it was last used, and maybe the workflow itself in a share link from the server.
Now, a shared prior workflow invocation would be best – to see inputs + workflow + outputs all together but I’m guessing you don’t have that anymore, so let’s start from what you have!
