Hi @Chandima1
Have you gone into your User → Preferences → Storage Dashboard area to review? Try checking for files that may be deleted but not purged.
You can follow the other areas to explore where you data may be located across histories with the Explore now buttons in the other two sections, too.
Once everything you need to be purged is marked, you can use the Refresh button on the top level again. The data will be purged and the quota space will free up within 24 hours (but usually sooner).
And since you are working at UseGalaxy.org, you already have access to the extra 1 TB of 30-day scratch space data storage area, too. If you are not sure where to find and use that, we have a guide here.
Any questions, please let us know. There was a small problem at the UseGalaxy.eu server earlier this week but that is resolved now. There are no known issues at the UseGalaxy.org server but we can follow up more if you think something is going wrong. Let us know! 