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Question: Bowtie2 not working
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gravatar for prashanth.klancy
4.2 years ago by
prashanth.klancy • 0
United States
prashanth.klancy • 0 wrote:

Dear sir,

i have uploaded some RNA Seq data and done with FastQc. I wanted to map the reads to mouse reference genome mm10 in bowtie2. I have been trying since two days, but its showing that the job is waiting to run. I have used bowtie2 in galaxy previously but never had this problem. Please let me know the solution or information on how to deal with it.

 

 

G Prashanth kumar

PhD Student

University of Hyderabad
waitingtorun status bowtie rna-seq datasets • 1.2k views
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modified 4.2 years ago • written 4.2 years ago by prashanth.klancy • 0
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gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Mapping jobs go to our busiest cluster and it is not uncommon for these to queue in the 'waiting to run' state. The most effective way to run jobs when this happens is to leave the queued jobs to process - do not stop and restart. More here:
http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

That said, two days is a bit long to wait. My guess is that these were started/restarted already one or more times, placing the new job at the back of the queue again. Or, that you had other jobs that were queued or running that were submitted before these, in the same history or another.

Jobs run in the order submitted, across your entire history. When the server seems to be busy, it is a good idea to submit your most important work first.

Good luck and hope this helps to explain how the queues work, Jen, Galaxy team
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for prashanth.klancy
4.2 years ago by
prashanth.klancy • 0
United States
prashanth.klancy • 0 wrote:

Thank you very much Galaxy Team
ADD COMMENT • link written 4.2 years ago by prashanth.klancy • 0
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