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Question: Bowtie2 samples still in queue after 48 hours
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gravatar for wcheng
12 months ago by
wcheng • 10
wcheng • 10 wrote:

Hello,

I am currently using Bowtie2 and my samples. 5 out of the 6 ran but one has been in the queue for at least 48 hours. I have also tried to change the cluster parameters to both jetstream and default galaxy but the sample still has not run. Do you think there is a problem with my fastq file that may be causing this to not get into the queue or is there potentially another problem?

Thank you
alignment bowtie galaxy chip-seq • 343 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by wcheng • 10
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I didn't find any queued jobs associated with your account at Galaxy Main https://usegalaxy.org, so these must have processed already if run there. If you are working on a different Galaxy server you should contact their administrators directly for advice.

The Galaxy Main clusters are very busy right now and larger jobs will queue longer than usual, some for over 24 hours, and possibly longer. The advice to allow queued jobs to stay queued, and to avoid deleting/restarting, is still true (this only extends wait time): https://galaxyproject.org/support/how-jobs-execute/

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