Hi @Dongqi_Xie
The original topic has an example history with all of the steps completed, so I think this is working unless there is a new problem. We can investigate!
XRef
The important part for the “no CDS” error is that those coding regions are originally provided from a known annotation source (Gencode, UCSC, RefSeq) that are later mapped onto any predicted annotation created (from Stringtie) during the discovery steps of the protocol.
If you didn’t included any known annotation yet, then that is where to start. If you did include known annotation but it didn’t seem to “map over” onto your final combined annotation from the discovery steps, we can probably help to resolve this. Most of the topics at this forum with the reference-annotation tag are about resolving similar data issues if you want to peek at what those look like first.
Then, would you like to clarify more about your situation? You could include: Are you following the tutorial methods exactly? Or using your own data? With the human genome assembly or a different species’ assembly? With a custom genome or using a server index?
You could also share back your history so far and we’ll be able to see those details, and maybe what is going wrong, plus learn the server you are working at and see the full error logs. How to share your work is here. → How to get faster help with your question
Let’s start there! 