Hi all, I have started a bowtie2 alignment (RNAseq, 100 bp paired end, two 15GB FASTQ files against hg19) yesterday, about 20 hrs ago, and the job is still waiting to start (grey boxes). I am wondering if this is normal, since previously, bowtie2 alignments for me usually started within a few minutes after the source files had become available. Should I just wait longer, or would you suggest I should cancel the current jobs and restart them? I noticed when I started the job yesterday I had some difficulties with galaxy, as connection to the server was unstable and the sites would time out frequently. Could this have caused some problems with job submission? Thanks for your help! Christian
If working at http://usegalaxy.org, then I can let you know that there were a few problems yesterday, now resolved. Also, the server is being restarted right now and that will "look" like a problem for a minute or so.
Allow jobs to stay queued. Queue times can vary, but if the server is busy (as it is now) certain jobs may queue for 24 hrs or a bit longer. Please see: https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute
Thanks, Jen, Galaxy team
Thank you so much for your explanation, Jen! Really appreciate it!
Update: The server had more changes today, so if you still have job delays or unexplained errors, try a re-run now. Jobs are queuing much quicker (right now - this might change depending on server load throughout the day/weekend).
Thanks, Jen! I re-started the job and this time it started running after just a few moments. It really must have been the server updates or bad timing (job submission during an update) that held my jobs in queue.