Workflow cannot run - Admin: older issue, see 25048 for current

Question: Workflow cannot run - Admin: older issue, see 25048 for current

23 months ago by

wuw111 • 80

wuw111 • 80 wrote:

I chose an uploaded workflow and clicked "Run workflow" on a selected input fastq file. A green box appeared and said:

"Successfully invoked workflow CartesianTnSeq_Step1_ClipIR_Trim25bp (imported from uploaded file). 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, nothing happened. No jobs in queue or running. No output.

I tried running different workflows but it was the same. I didn't hide output in the workflow.

Any help?

Thanks.

workflow • 1.8k views

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modified 8 months ago by a.januszewski • 10 • written 23 months ago by wuw111 • 80

Is the box checked "Send results to a new history " just above the ' Run workflow' button you use to start the workflow?

If it is then you do not expect to see any datasets (jobs) to be created in the history you started in. You will need to look at the 'view al histories' view and look at the new histories created.

ADD REPLY • link written 23 months ago by Guy Reeves • 1.0k

Having the same issue. I can successfully queue and run single jobs. Workflows still don't queue. So if our requests aren't showing up on the current history as queued datasets does that not mean that the request to run a workflow is not making it to the server?

Thanks

ADD REPLY • link written 23 months ago by peterristow • 10

Is the box checked "Send results to a new history " just above the ' Run workflow' button you use to start the workflow?

Are you using usegalaxy.org?

ADD REPLY • link written 23 months ago by Guy Reeves • 1.0k

I tried both options. No "new history" or queue are generated when invoking workflows.

Sorry, yes I am on usegalaxy.org.

ADD REPLY • link written 23 months ago by peterristow • 10

Hello this problem just started occurring for me today and it started suddenly. I quickly ran the same workflow three times on three datasets - and the first and third were added to history but not the second. And since then it's just stopped completely. I retried running workflows five or six times and one went through for some reason. I've tried different workflows, different histories, refreshing the history, refreshing the webpage, reloading the history. Nothing works. I am positive that the "send to new history" option is not checked. Has anyone found a solution to this?

ADD REPLY • link written 21 months ago by zachary.gaber • 80

23 months ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

We've now applied a fix to main and workflows are scheduling correctly. Please don't rerun workflows yet, your existing workflow invocations should get processed shortly.

ADD COMMENT • link modified 22 months ago • written 23 months ago by Dannon Baker ♦ 3.7k

(updated the parent reply)

ADD REPLY • link modified 22 months ago • written 22 months ago by Dannon Baker ♦ 3.7k

23 months ago by

weishwu • 20

weishwu • 20 wrote:

I posted the question. I didn't let it send to another history. I actually tried sending it to another history. But there is no sign of job running either way. I tried different workflows, and even a one-step workflow which is only fastq grooming, but there is no sign of job running or queueing anyhow. I tried refreshing history. No difference.

ADD COMMENT • link modified 23 months ago • written 23 months ago by weishwu • 20

that is strange. are you logging in as a registered user ? If you are I do not really have any more ideas can you share the workflows and dataset on use galaxy? If you do I will try wth my account. Cheers Guy

ADD REPLY • link modified 23 months ago • written 23 months ago by Guy Reeves • 1.0k

Workflow: https://usegalaxy.org/u/mapped%20reads%20in%20illumina%2011/w/20131219clipirtrim25bp-imported-from-uploaded-file-1

History: https://usegalaxy.org/u/mapped%20reads%20in%20illumina%2011/h/test

Let me know if you can't get them.

Thanks for looking into this!

ADD REPLY • link written 23 months ago by weishwu • 20

23 months ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

If you manually refresh the history panel, do these jobs show up?

ADD COMMENT • link written 23 months ago by Dannon Baker ♦ 3.7k

23 months ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

I'm also seeing (simple and small) workflows not running on Main.

If I choose to run a workflow in a new history, the history is generated, but the jobs don't appear. If I run the workflow within a history the jobs also don't appear.

Cheers, Mo Heydarian

ADD COMMENT • link written 23 months ago by Mo Heydarian ♦ 830

23 months ago by

june.deng • 10

june.deng • 10 wrote:

I am experiencing the same problem here

ADD COMMENT • link written 23 months ago by june.deng • 10

22 months ago by

carlos.perezarques • 10

carlos.perezarques • 10 wrote:

I have the same issue. Any news?

ADD COMMENT • link written 22 months ago by carlos.perezarques • 10

22 months ago by

KaYi.Chan • 10

KaYi.Chan • 10 wrote:

I am also experiencing the same problem since last week. I thought it could be because I'm trying to analyse human whole genome which is huge therefore galaxy doesn't support. Then I tried analyse E.coli whole genome (which I know it worked before) but nothing happens. Does anyone know if it has been resolved? Thanks.

ADD COMMENT • link written 22 months ago by KaYi.Chan • 10

23 months ago by

radhika.patel • 0

United Kingdom

radhika.patel • 0 wrote:

Hello,

Is there any update on this problem being fixed? I have been having the same issue for the last 3 days.

Thanks, Radhika

ADD COMMENT • link written 23 months ago by radhika.patel • 0

It was fixed briefly, but the problem seems to have resurfaced. I'm going to have to do more digging to fix this, sorry for the delay.

ADD REPLY • link written 23 months ago by Dannon Baker ♦ 3.7k

Hi, I am also experiencing this for the past week.

ADD REPLY • link written 22 months ago by KaYi.Chan • 10

14 months ago by

cwalker912 • 0

cwalker912 • 0 wrote:

I noticed this post from a few months ago and am having the exact same issue now. Was this ever resolved? Is it just a sporadic issue. I am trying to run on galaxy main.

ADD COMMENT • link written 14 months ago by cwalker912 • 0

There is a new issue that we are actively working to correct. Please follow the primary open question for this for updates https://biostar.usegalaxy.org/p/25048/

ADD REPLY • link modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson ♦ 25k

8 months ago by

a.januszewski • 10

a.januszewski • 10 wrote:

I am having the exact same issue now and I see has been an issue in the past.

I am running on galaxy main. Any ideas?

Thanks

Adam

ADD COMMENT • link written 8 months ago by a.januszewski • 10

Hi Adam, please see: https://biostar.usegalaxy.org/p/27087/#27090

If you need more help, let's follow up in that thread ^^ since while the behavior may seem the same, the underlying cause of the invocation/execution issue is different (not a software problem, but rather a usage issue).

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