Active (green) History dataset: unable to use as input as tools say it was deleted

usegalaxy.org support
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I did some cleaning of my histories recently and deleted and purged several items/histories so I could run new tools. I did not delete a dataset containing a list with 302 fastqsanger.gz pairs. The dataset is green. I can click on it/open it and see all 302 fastqsanger.gz pairs. However, if I try to use it as input for a tool (FASTQC) I get this error message: “parameter ‘input_file’: the previously selected dataset collection has elements that are deleted.” I copied the dataset to a new history but received the same message. I cannot undelete any elements as all 302 pairs are there and green.

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HI @Laura_Peirson

I’m guessing that you deleted/purged some of the hidden datasets in that original history. Let’s see if we can fix things up.

What to try

  1. With that collection in a brand new history
  2. Click on the pencil icon for the collection and try to do something with it. I would suggest changing fastqsangergz to uncompressed fastqsanger. FAQ: Changing the datatype of a collection
  3. This will reset some metadata on the collection and might be enough. Missing implicitly converted data would be recreated – so this is what I’m asking you to try for.
  4. But if the original compressed is actually gone, that will fail too, and you’ll need to load that data again.

Next time.

  1. When deleting a collection, you can use the drop down to choose to delete the collection and the datasets inside of it (the hidden elements) as a safer way to navigate the cleanup.
  2. You could also copy the individual datasets or collections you want to keep into a new history – moving the top level collection folder moves the whole thing (including hidden).
  3. Then, purge the old history.
  4. In short, never go into the hidden tab since it is such a complicated area to pick through (for anyone).
  5. Delete from the active tab only, then use the “purge all deleted” pull down menu or the Storage Dashboard to do the purging.

Please let us know how this goes! :slight_smile:

Update: I’ve sent you a direct message to share your history link inside of. Let’s confirm my guess about what is going on! Thanks!

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Update: Resolved. Navigating into the collection folder did show that the datasets inside were purged.

The best advice we have for everyone:

  1. Delete datasets in the History from the active tab only.
  2. You can undelete or purge individual datasets in the deleted tab.
  3. Or, you can undelete or purge datasets in a batch using history functions or with the Storage Dashboard.
  4. Avoid manipulating datasets in the hidden tab directly. Access is for a convenience or review purpose. These files have special meaning and are very difficult to navigate! If there is some reason why that is needed, please bring that up as a new question and we can help you to come up with a safer way to get that same action done.

Thanks everyone! :slight_smile:

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Okay, thanks. I will import the data again. Best regards.

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