I began running several ht-seq count analyses on Monday, October 16th. Since then they have appeared in my history but still are grey and show a small clock in the corner which I'm assuming means they have not began to run. I have encountered several problems like this in the past where I submitted a task and it never ran (even after waiting for several weeks to a month). Any assistance/insight into this issue would be greatly appreciated!
The input Tophat jobs each have a metadata problem that must be corrected before used as input to downstream tools. Click on the link in the yellow box of the expanded datasets to reset the metadata. Tophat is known to produce datasets in this state, which can complicate using it. Tophat is considered deprecated with HISAT2 being the replacement.
That advise is for the current jobs that are queued. For prior delays, especially if that long, I suspect there was also some type of input problem but cannot confirm that. However, if it comes up again and you are waiting more than 2 days, please let us know and we can help check to find out what is going on.
Galaxy tutorials, several of which include HISAT2 with example settings for different use cases: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team