Welcome @Monish_V
If the Intersect the intervals of two datasets tool is failing, it might be for resources reasons since this type of operation can create some very very large outputs! Putting the largest file into the second input section on the form can help sometimes, so please consider trying that way if you haven’t already.
Other than that, this could just be a data format problem. You could try cutting out the columns you are joining on, then running some summaries on them to double check. Or, use the Group tool to summarize. Ideas about tools to try are here → Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses with more in the tool panel.
If you get stuck and would like help troubleshooting this, you can share your history with the error and your tests and we can try to help more here! It is hard to guess without seeing the example. You can post the history share link, screenshots, or other details back here. → How to get faster help with your question
Now, there were some server issues earlier in the week, but those should be resolved. But that is part of what we can help to check.
Let us know if you figure this out or if we can help more! 