CUFFDIFF in Galaxy not working for past few days

Question: CUFFDIFF in Galaxy not working for past few days

2.1 years ago by

I have been using Galaxy webserver at usegalaxy.org for my works, and suddenly for the past few days I am unable to run CUFFDIFF successfully. The input pages are coming correctly, but no output files are created.

I have used CUFFDIFF in galaxy previously and this is the first time I am encountering such a problem. I even tried changing the version but it was of no use. CUFFMERGE, CUFFLINKS etc seem to work fine.

Please help.

tool queue job usegalaxy.org cuffdiff • 768 views

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modified 2.1 years ago by Mo Heydarian ♦ 830 • written 2.1 years ago by devikaparvathy • 10

2.1 years ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

Hi Devika,

Please check the first options on the Cuffdiff tool form. If I set "Omit Tabular Datasets" to "Yes" and "Generate SQLite" to "No", I see the scenario you describe above, as Cuffdiff has been told to discard the tabular output files and to not generate a SQLite database, resulting in no output files. Check if these were the settings used and if changing them provides the output you normally see when using this tool.

Hope this helps!

Cheers,

Mo Heydarian, Galaxy Team

ADD COMMENT • link written 2.1 years ago by Mo Heydarian ♦ 830

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There were server issues earlier in the week and this created a job backlog at Galaxy Main for certain tools (Cuffdiff is one of them). Allow grey jobs to remain queued- this will ensure they execute quicker since are already in the queue in line waiting for a cluster node to open up. Deleting and restarting places jobs in the back of the queue, which everyone wants to avoid. https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

If the problem is different and the job is failing, please submit a bug report and we can examine your history to see what is going on. There are currently no known issues with the tool. Please include a link to this post in the comments. How to: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks and sorry for the recent job delays. The wait time has been progressively getting shorter since Mon/Tues and the server is expected to restore to normal queue times in a few days.

Jen, Galaxy team

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

2.1 years ago by

devikaparvathy • 10

devikaparvathy • 10 wrote:

Hello,

Thank you for the reply. But the issue seems slightly different in that, the jobs are not even being added (No new datasets added to the history pane)

Only the following message is shown - (but there is no list of the new datasets that is usually shown alongwith)

"1 job has been successfully added to the queue - resulting in the following datasets:

You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered."

However there is no indication of the new datasets/the CUFFDIFF job anywhere.

ADD COMMENT • link written 2.1 years ago by devikaparvathy • 10

Did you refresh the history pane? Click on the double circle icon at the top to do this.

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

I took at look at your account. In the two histories used in the last 4 days, neither has any Cuffdiff jobs in the history.

Maybe try the job again today? My guess is that the server was busy timing out the submission or the job once submitted was not allowed to fully complete that operation (navigating away from the form before launch could cause that). Rerunning will probably solve the problem.

If it doesn't launch again, take a screenshot of the tool form as filled in for submission (a few if needed to capture the entire form and all options), generate a link to the history, capture a link to this Biostars post, and put all of that information into an email to galaxy-bugs@lists.galaxyproject.org. We'll see if the failure of the job to launch is reproducible using your exact inputs/params and go from there. No other reports of this problem have come in. If it is a novel, investigating is important.

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

2.1 years ago by

devikaparvathy • 10

devikaparvathy • 10 wrote:

Tried that too and also tried logging in and out many times. Usually once the task is submitted, the main page itself lists out the numbers and list of new datasets that will be generated. Here I am not even getting that. Is there anyway I could share my activity/ page to show you what's happening?

ADD COMMENT • link written 2.1 years ago by devikaparvathy • 10

See my comment to the earlier reply.

I understand what is happening and it could be a database delay of some type. Try running again first and stay on the form until submission is completed (showing the expected content you mention).

If that fails, send in the info to the galaxy-bugs list please.

Thanks! Jen, Galaxy team

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

2.1 years ago by

devikaparvathy • 10

devikaparvathy • 10 wrote:

Hi thanks. I have mailed with all necessary details to the galaxy bugs list.

ADD COMMENT • link written 2.1 years ago by devikaparvathy • 10

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