The galaxy websites, pops up following message frequently, Will I also miss the data currently being processed while getting this message or it will be saved in the server? The message is "Cannot connect to Galaxy Galaxy is currently unreachable. Please try again in a few minutes. Please contact a Galaxy administrator if the problem persists."
This was an intermittent problem yesterday at Galaxy Main https://usegalaxy.org due to a very high server load.
When this comes up, it usually indicates a connection delay/timeout (server-side), pop-up warnings last for a very short time (few minutes at most, with a few seconds more common), and importantly, does not impact jobs that are already queued or running in your account.
We were also adding in the last set of upgrades for the newly released Galaxy version 18.05 yesterday (which involves server restarts). These also do not impact jobs and can sometimes trigger short connection pop-ups. https://docs.galaxyproject.org/en/master/releases/index.html
Small tunings for the new release (as needed) combined with the server load issues might cause more pop-up interruptions than usual short-term, but all should also resolve over the next few days.
Tophat is a deprecated tool. Please consider using HISAT2 instead.
Galaxy tutorials: https://galaxyproject.org/learn/
Thanks for reporting the problem and sorry for the inconvenience!
Jen, Galaxy team