Question: Workflow cannot run
9
gravatar for wuw111
4 months ago by
wuw11190
wuw11190 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 • 507 views
ADD COMMENTlink modified 3 months ago by zachary.gaber60 • written 4 months ago by wuw11190

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 REPLYlink written 4 months ago by Guy Reeves850

Hi

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 REPLYlink written 4 months ago by peterristow10

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 REPLYlink written 4 months ago by Guy Reeves850
1

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

Sorry, yes I am on usegalaxy.org.

ADD REPLYlink written 4 months ago by peterristow10
4
gravatar for Dannon Baker
4 months ago by
Dannon Baker3.6k
United States
Dannon Baker3.6k 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 COMMENTlink modified 4 months ago • written 4 months ago by Dannon Baker3.6k

(updated the parent reply)

ADD REPLYlink modified 4 months ago • written 4 months ago by Dannon Baker3.6k
2
gravatar for weishwu
4 months ago by
weishwu20
weishwu20 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 COMMENTlink modified 4 months ago • written 4 months ago by weishwu20

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 REPLYlink modified 4 months ago • written 4 months ago by Guy Reeves850

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 REPLYlink written 4 months ago by weishwu20
1
gravatar for Dannon Baker
4 months ago by
Dannon Baker3.6k
United States
Dannon Baker3.6k wrote:

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

ADD COMMENTlink written 4 months ago by Dannon Baker3.6k
1
gravatar for Mo Heydarian
4 months ago by
Mo Heydarian600
United States
Mo Heydarian600 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 COMMENTlink written 4 months ago by Mo Heydarian600
1
gravatar for june.deng
4 months ago by
june.deng10
june.deng10 wrote:

I am experiencing the same problem here

ADD COMMENTlink written 4 months ago by june.deng10
1
gravatar for carlos.perezarques
4 months ago by
carlos.perezarques10 wrote:

I have the same issue. Any news?

ADD COMMENTlink written 4 months ago by carlos.perezarques10
1
gravatar for KaYi.Chan
4 months ago by
KaYi.Chan10
KaYi.Chan10 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 COMMENTlink written 4 months ago by KaYi.Chan10
0
gravatar for radhika.patel
4 months ago by
United Kingdom
radhika.patel0 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 COMMENTlink written 4 months ago by radhika.patel0

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 REPLYlink written 4 months ago by Dannon Baker3.6k

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

ADD REPLYlink written 4 months ago by KaYi.Chan10
0
gravatar for zachary.gaber
3 months ago by
United Kingdom
zachary.gaber60 wrote:

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 COMMENTlink written 3 months ago by zachary.gaber60
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