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Question: Prolonged - Job Waiting To Run
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gravatar for Veranja Liyanapathirana
5.6 years ago by
Veranja Liyanapathirana • 70
Veranja Liyanapathirana • 70 wrote:
Dear Galaxy team,   I am running short read alignments with Bowtie for illumina using some data generated from split data using barcode splitter. The alignment programme has been indicated the "job waiting to run" status for nearly over an hour. I can meanwhile perform other functions such as data uploading and trimming, splitting etc where the job is continued and completed.   Thank you, Kind regards, Veranja   Veranja Liyanapathirana, Graduate Student, CUHK
alignment bowtie • 1.0k views
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modified 5.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.6 years ago by Veranja Liyanapathirana • 70
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gravatar for Jennifer Hillman Jackson
5.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Veranja, This sounds like normal behavior - so everything is OK. When a job is waiting (grey) that means it is in the queue, waiting to process. It will run in the order it was started with respect to the jobs started by other users also running jobs on the public Main Galaxy instance. It is important to not stop/restart the job or you will lose your position in the queue and move back to the end - the best strategy is to just leave the job alone and let it run. Different jobs types run on different clusters (with different queues) - so that is why you are seeing other job types complete. They are executing on a less busy cluster. In germinal, mapping and other NGS jobs will take more time to queue/execute than non-NGS jobs, but this is not 100% true for all cases, just a guideline. Hopefully this helps! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
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