Ran Tophat 5X on same data set that worked 2 days ago… Is Tophat down? I have deadlines to meet…
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hi @rpotens007
Are you working at Galaxy Main https://usegalaxy.org?
If yes, then there are known issues with some mapping jobs. Choosing a specific cluster to run the jobs on will help until the issues are fully resolved.
Ticket about the problem (will close out once fixed): https://github.com/galaxyproject/usegalaxy-playbook/issues/257
Workaround with details about how to target the proper cluster is linked from that ticket above, but here is the post directly: HISAT2 Not working
This is a priority correction and we expect a full resolution soon.
Update: Fixed
Note to all end users running mapping: Using all defaults for the “Job Resources” parameter is a good choice now again. No need to target a particular cluster anymore. Allowing Galaxy to choose the target cluster based on the currently available resources, at the time of job submission, is the fastest way to run tools.
Ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/257#issuecomment-540676708
Hi Jennifer,
Thank you for addressing the mapping issue. Looks like it is working fine.
Renee
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Super, thanks for letting us know 
I am unable to get TOPHAT to work the past several days. It churns away and finally i get an error message. Is it still supported?
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Tophat has been deprecated for many years now. It is not maintained anymore and could present with issues at any time. We were able to get a workaround before, but that may no longer be possible, or if fixed, it won’t be soon.
Everyone needs to migrate away from using Tophat. HISAT2 is the replacement.
Prior Q&A that covers alternatives: