Hi @zrs1
When using public Galaxy servers (or really, any Galaxy server), it is best to leave queued jobs queued. Each will start up as resources become available. Avoid deleting and restarting, unless you need to modify inputs/settings, or you’ll lose the original placements in the job queue, further extending wait time.
The usegalaxy.org server and many other public servers are very busy right now. Mapping jobs require the use of larger cluster nodes which tend to be the busiest. It will take some time to process all 96 jobs.
More details about how jobs queue and execute are in this recent Q&A: Job Stuck in Queue
Alternatives include setting up your own Galaxy server. These prior Q&A topics have basic details and link-outs to all options. A commercial cloud is not your only choice but does involve less administration/local resources. Commercial servers -- Galaxy Choices && Galaxy Cloudman or GVL?.
To find more Q&A about Galaxy choices, please search this forum with the keyword “choices” or “cloudman”.
Thanks!