There is some problem with the inputs. Try comparing your methods with those in our tutorials.
These cover many types of RNA-seq analysis workflows/tools. In particular, review these:
I’m not sure which tool you are using or where you are running it, but tool forms usually have much help included that can help to sort out issues.
Just as a guess, I suspect the problem is with the identifiers used in one or more of your inputs. But the issue could be rooted in some other issue, including the output from prior tools (including limma). Maybe some data is missing? Example public Q&A post that covers this type of python error. It is a bit dense but the examples are worth reviewing – the main point is that data is not matching up as expected at some step during processing.
If you cannot figure out the issue and are working at a public Galaxy server, you could also send in a bug report from the error dataset for more direct feedback. Please be aware that sending in a bug report is usually the slowest way to resolve problems due to inputs … reviewing your own data and comparing to tool help/tutorials is much faster.