Job En-Queued, But Not Running

Question: Job En-Queued, But Not Running

6.3 years ago by

Vijaykant N • 10 wrote:

Hi, I created a workflow ( https://main.g2.bx.psu.edu/u/vijay-uky/w/rna-seq-analysis ) and uploaded the reference genome (30 MB FASTA file) and the reads (45B FASTQ file after running the FASTQ groomer). Once I ran the workflow on the public server, it will enqueue the needed output (steps) but the job just wouldn't run. I tried to run the same on a local instance at my lab, it works fine. Was curious to know if there is some issue with running tools such as TopHat, Cufflinks and Cuffcompare. If you could let me know, would greatly appreciate. Sincerely, Vijay

rna-seq cufflinks • 1.4k views

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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Vijaykant N • 10

6.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Vijay, 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. The size of any particular job does not place it in the queue ordering - only the time that it was initiated. I can see that your earlier jobs completed and that a new set from today have been queued. The RNA-seq tools are among the most popular as well as the most resource intensive and the public server is usually busy with this job type. We have processes in place to ensure fair access. Leaving your jobs in the queue is still the best option if you wish to run them on Main, but if your work is urgent, Local or Cloud instances are alternatives. CloudMan http://usegalaxy.org/cloud Local (for others following thread) http://getgalaxy.org Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Lew, CC'ing the galaxy-user list because I am assuming that your question is about the free public server ("Main") @ usegalaxy.org / main.g2.bx.psu.edu. If you have any future questions about Main, please post them to Galaxy-User so that others can see the question and respond. If I am reading the qstat output correctly, there are currently ~140+ jobs in the NGS queue, which means that Main is currently under very heavy load. The best thing to do is let the jobs sit in the queue. Killing and restarting them bumps them to the end of the queue. We are currently discussing a number of options for letting users know in situations like this, that while the job is not currently running, it is in the queue, and is moving forward. Thanks, Dave C PS: and the number of jobs in the queue has dropped by 2 since I started typing this email. -- <http: galaxyproject.org="" wiki="" gcc2012="">http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

ADD REPLY • link written 6.0 years ago by Dave Clements ♦♦ 2.5k

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