Hello John, When the public Main Galaxy server is busy, jobs will be in a grey "waiting to run" state while they are in the queue waiting to run. How long this takes can vary. Allowing the job to stay in this state (not deleting/restarting) is the best option to preserve your place in line. Different job types will go to different queues, so there could be cases where some jobs run and some stay in a queue. I can tell from one of your histories that this is the case - where a FASTQ file filtering job went to one queue and mapping jobs (lastz and Bowtie) went to another queue before being deleted. These jobs appear to be less than 24 hrs old - and more likely around 12. I can let you know that this is within the queue window for a NGS mapping job when Galaxy is very busy. FTP is unrelated to this job distribution process and there are currently no known issues (I just ran a double check and a test upload was fine), so please try FTP upload again and send more details if problems persist. http://wiki.g2.bx.psu.edu/FTPUpload If your work is urgent, a local or cloud instance is recommended: http://getgalaxy.org http://usegalaxy.org/cloud Hopefully this helps, Jen Galaxy team On 8/8/12 5:33 AM, John Clayton wrote:

Dear Sir or Madam,

My recent jobs submiteed to the Galaxy server mapping short reads using the LastZ tool do not start processing. They remain grey after I hit execute and remain indefinitely in the queue even while I am able to start additional jobs subsequently. Do you have any idea what is going on here? I used LastZ before and it worked fine.

Many thanks,

John

-- Jennifer Jackson http://galaxyproject.org