I have some problems for running galaxy tools (tophat, cuffdif,..), while I am under the quota (using 120 Go). Galaxy does not work on our data, for example, aligment with tophat using 2 fastq files (paired end) is waiting for running since yesterday afternoon. Is Galaxy stopped?
Your queued job should now have completed. There was an error with status checks between Galaxy and the cluster which meant that while your job was dispatched and ran, Galaxy was not notified when it completed. It also appears that Galaxy failed to set metadata on the output(s). You should be able to remedy this by clicking the "auto-detect" button on the dataset info page. We are looking in to the cause of these failures.
Sorry for the inconvenience, thanks for using Galaxy!