Dear Galaxy Team,
I've been very impressed over the last few months with the speed, ease, and user accessibility you have created. However, I have recently been stumbling over the same error message: Remote job server indicated a problem running or monitoring this job. I first encountered this as I tried going back and updating my FASTQ RNA-Seq runs with hg38, as it is finally similar between UCSC and Ensembl. However, I see the tophat job run (yellow), take a bit of time (normal), and then it removes itself and states that it is waiting to run (odd). After ~24 hrs or so, it then states this error message.
Perhaps it is my run of tophat? Everything else seems to work just fine without this error. It actually first started when I added in manually the reference genome hg38, as I ran into a previously reported cuffmerge error that prevents the user from selecting a reference genome from galaxy's cache when multiple files are selected to be merged together.
Thanks in advance!