Question: Any computation limit? Bowtie2 job has been waiting for hours
gravatar for ztzou
13 days ago by
ztzou10 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 • 51 views
ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson23k • written 13 days ago by ztzou10
gravatar for Jennifer Hillman Jackson
13 days ago by
United States
Jennifer Hillman Jackson23k wrote:


When working at, 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 COMMENTlink written 13 days ago by Jennifer Hillman Jackson23k

That makes sense. Thanks!

ADD REPLYlink written 13 days ago by ztzou10

Hi Jen,

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

ADD REPLYlink written 11 days ago by ztzou10

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 REPLYlink written 11 days ago by Jennifer Hillman Jackson23k
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