Cufflinks never start??

Question: Cufflinks never start??

2.1 years ago by

I am still a newbie on Galaxy.

I mapped my RNA-seq reads by TopHat without problem (I believe), then I fed the output "accepted hits"to Cufflinks. Four jobs popped up on the history window, then they have been "grey" for several days. I canceled the job and retried but it never work.

Some other jobs I queued after the Cufflinks jobs finished without problem. So my Galaxy hasn't been stuck.

What is the problem?

Please help.

Thanks.

grey-datasets delays usegalaxy.org jobs • 723 views

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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by 柴田弘紀 • 20

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The server http://usegalaxy.org is most likely just busy or you had many jobs associated with your account queued. That said, this long of a wait is unusual. If something more is going on server-side - we will write back with an update.

Please know that other issues can be a factor. Inputs (incorrect format, empty inputs, metadata issues), custom reference genome formatting, many compute intensive jobs queued .. these usually result in job failures or unexpected results. Should job delays continue and you can't find the source of the problem or simply want feedback, please feel free to send in a bug report. Include a link to this post in the comments. We'll check the entire history, not just the specific problem reported. Make sure the data to be examined is undeleted. Or, you can use the self-help troubleshooting list linked below that covers the basic checks - these are the same checks we do here for reported problems.

Note that reruns extend wait time https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute
Routine checks performed on reported bugs. You can do the same to expedite corrections - if any are needed: https://wiki.galaxyproject.org/Support#Error_from_tools
Use if you need more feedback: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks for reporting the issue. Different jobs are sent to different clusters. This is probably why other jobs started while the Cufflinks jobs were still in queue (these are dispatched to a busier cluster). I suggest allowing these to run, even if it takes a few days. If that advice changes, will include help in the updated reply (should server issues or longer-than-normal queues are present right now).

If you are not using http://usegalaxy.org, reply with details: Local or cloud Galaxy? Some other public server (URL)? Private Galaxy? (For the last two - contacting the admins of that instance is the path toward finding out what is going on.

Best, Jen, Galaxy team

ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thanks for your reply. I am working on http://usegalaxy.org. I am using built-in mm9 for the reference genome. The size of my "accept hits" is only 212.2MB. I guess it's not too big. Still the jobs are "grey". How can I get bug reports??

Best,

Hiroki

ADD REPLY • link modified 2.1 years ago • written 2.1 years ago by 柴田弘紀 • 20

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Update: The problem was on our side. The cluster fix has been made and jobs are dispatching normally. Queued jobs will execute - no need to delete/rerun. Tools that require more resources are sent to a busier cluster. That queue is expected to have some continued delays until the backlog of jobs is processed (up to a few days).

Thanks for reporting the problem and for your patience, Jen, Galaxy team

ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks for your help! Still my jobs haven't started running. But I will wait a bit more:)

Hiroki

ADD REPLY • link modified 2.1 years ago • written 2.1 years ago by 柴田弘紀 • 20

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