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Question: Any computation limit? Bowtie2 job has been waiting for hours
1
gravatar for ztzou
12 months ago by
ztzou • 10
ztzou • 10 wrote:

Hello. I submitted a job on Galaxy using Bowtie2 to map DNAseq reads onto sacCer3 reference genome 6pm (UTC) today and it is still waiting in queue. Is this what I should expect since I've been using Galaxy these days, or due to other reasons? Thanks!
bowtie galaxy • 428 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by ztzou • 10
0
gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When working at https://usegalaxy.org, jobs can queue up to 24 hrs during the busiest times yet most will start up quicker. Factors include the job/tool type, how busy the clusters are, and how many jobs are launched at the same time.

You are still in the normal queue time frame for a mapping job (~ 4 1/2 hrs so far). Leave the job queued and avoid deleting/restarting as that just extends the wait time (job is added back at the end of the queue).

Jobs execution FAQs:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k

That makes sense. Thanks!

ADD REPLY • link written 12 months ago by ztzou • 10

Hi Jen,

My job is still in the queue. I guess this is abnormal?

ADD REPLY • link written 12 months ago by ztzou • 10

Many users have jobs that are queued right now, some for over a day. I have asked our admin for another update.

For now, leave queued jobs queued. Even if it turns out there is a problem, delayed queued jobs are generally found and eventually processed. Stopping and restarting is rarely the solution.

I'll mark this for an update if more is going on.

Sorry for the problems!

ADD REPLY • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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