The issue seems to be that datasets have been deleted, but not permanently deleted (purged). Data needs to be purged before it is actually removed (and no longer recoverable, even by an administrator).
Try clicking on the “186 deleted” toggle at the top of the left history panel.
If a dataset has only been deleted but not permanently deleted (purged) you’ll see a message within the dataset with note/link to purge.
Since you have so many datasets and are removing all in the same history, individually clicking on those links, or even using the “Operations on multiple datasets” function, will take more time to do.
Two shortcuts, either should work:
- Permanently delete (purge) the entire History. Do this from the User > Histories view. The pull-down menu per history has an option for “Purge History”. Or, you can select multiple histories and use the “Delete Permanently” button at the bottom of your history list to purge in batch.
- Permanently delete (purge) all datasets that are deleted but not permanently deleted, in batch, using the History menu function “Purge Deleted Datasets” in the Analyze Data view (the view in your screenshot).
- Histories cannot be in a shared state if you want to permanently delete (purge) them. Unshare as needed first.
- Purging is a two-step process using any method. A pop-up box is the second step. Click to confirm the action.
- When purging a large amount of data, the server may take some time to update and accurately reflect quota usage. You can wait, or you can speed up the process by logging out then logging in again.
FAQ with full details: https://galaxyproject.org/support/account-quotas/
I also added some tags to your post. Click on them to review prior Q&A about the topics. You can also search all topics with the keyword “purge”. Many have screenshots that may help even more.
Please give this a try and let us know if you need more help.
Thank you very much!