Question: (Closed) HISAT2 program does not complete
gravatar for bkasinat
10 weeks ago by
bkasinat0 wrote:


I'm having the same problem--my HISAT2 programs fail to complete after days of running. I tried rerunning the program with the target cluster set to Jetstream and it's still in gray. Is there anything else I can try?


rna-seq queue job galaxy • 81 views
ADD COMMENTlink written 10 weeks ago by bkasinat0

Hello bkasinat!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: Avoid restarting jobs as this only extends wait time. See the prior post for FAQs and more details about how jobs run.
ADD REPLYlink written 10 weeks ago by Jennifer Hillman Jackson25k

Part of the delay had to do with cleaning up the deleted/rerun datasets. I don't see any jobs queued anymore. And those that had the inputs deleted are now green at the collection level, but blue (paused) at the dataset level. This is because the inputs were deleted before the job completed.

For the next runs, be sure to leave the input datasets active while the job is queued/executing. Once completed and the result confirmed to be correct, you can delete/purge inputs to recover quota space as needed. Be sure to save copies (downloads) of any data that you may want to work with again before permanently deleting/purging -- it will not be recoverable within Galaxy. Only active and deleted (but not permanently deleted) data can be recovered -- and that data does count toward quota (in either state).


  • Datasets and how jobs execute
  • Checking for active vs deleted vs permanently deleted (purged) datasets and histories
ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Jennifer Hillman Jackson25k
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