I am running Cufflinks of a couple of dozens of RNAseq Bam files from using mm9 as a reference. First 10 or so went well, but now Cufflinks of two Bam files are running (yellow colored) for >16 hours and it does not seem to be completed. I understand that the processing time depends on the load on the server CPU, but could there been something wrong that causes the delay? These Bam files are either from TopHat in the same history, or uploaded Bam from previous analyses. The particular two files are directly from the TopHat. Thank you so much for your advice.
To see the current state of jobs, try refreshing the history panel. Do this by clicking on the double circle icon at the top of the right history panel.
If a job is running, allow it to complete. The jobs are simply larger ones.
If any jobs should fail later on for resource (complete and turn red, instead of green), double checking the inputs is the first thing to try. See section 2.7 and 2.8 in the wiki: https://wiki.galaxyproject.org/Support
Thanks, Jen, Galaxy team