I'll reply to your bug report, but just for general information to
others, the most common cause for delays is that the Galaxy main
is busy and/or the job itself large.
Jobs can be queued ('grey') for up to a day when we are at peak usage.
It is important to not stop/restart jobs at this stage, otherwise they
move to the end of the queue again. Once running ('yellow'), a job
as Tophat has normally up to 72 hours to complete. How long a job will
run depends on the type of job, the parameters used, and the size of
Should there be a job size issue, the job will error out, often
indicating that it is too large to run on the public Main instance
sometimes any instance) due to the parameters selected and the inputs.
In these cases, the next step is reviewing the parameters and inputs,
making adjustments, and then determining if a cloud solution with more
resource (often memory) is a potential solution worth testing out.
If jobs are urgent, a cloud or local solution is also an option, large
or small. Which to choose depends on what resource you prefer or have
Occasionally there are other factors. Please feel free to write in, as
you have done, with a bug report to check in and see if this is the
Good question and I will be getting back to you shortly about your