Workflows don't execute after successfully being invoked at https://usegalaxy.org -- RESOLVED

Question: Workflows don't execute after successfully being invoked at https://usegalaxy.org -- RESOLVED

4 months ago by

jomiles26 • 50 wrote:

I've been trying to execute two workflows on several of my datasets, but they won't execute. I get the message to say that they've successfully been invoked, but then nothing happens and no new datasets are generated - either in the current history, or in a new history. I'm not close to my data quota either (42 of 250 GB used on Galaxy Main). Could this be a problem connecting with the server? If so, what can I do about it?

The workflows I'm using are:

CloudMap hawaiian variant mapping with WGS and variant calling workflow (no candidate genes)
VCF to snpeffs uwml

workflow usegalaxy.org galaxy • 741 views

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modified 6 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by jomiles26 • 50

I've run both of these workflows successfully before - they just suddenly stopped working today. The cloudmap workflow is:

https://usegalaxy.org/workflow/display_by_id?id=d99d0984a42d9837

And the other is:

https://usegalaxy.org/workflow/display_by_id?id=824b6205aa40ff3b

ADD REPLY • link written 4 months ago by jomiles26 • 50

I ran into some other problems with workfow tests, too. Our admin is out today, so it may not be until Monday when we get back to you with more (noting a fix or a link to an issue ticket).

Thanks for reporting the problem and sorry for the current inconvenience! Jen

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Update: We can confirm the problem with workflow execution. This is the issue ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/151

The current execution problems just started late last week and impact all workflows (new or existing). We are working on a solution. As we work through the problem, technical details and possible workarounds will post both to the issue ticket. Once resolved, both will also be updated and closed out.

If others have questions about this same problem, review this post and the issue ticket first. Should you want or need to comment that you are also running into the issue, that is fine, but please do not post as an answer - instead post as a comment. Please do not start another duplicated post.

Thanks again for reporting this, it is new. Jen, Galaxy team

ADD REPLY • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Ok, thanks for keeping me updated.

ADD REPLY • link written 4 months ago by jomiles26 • 50

The problem is still ongoing. July 25.

ADD REPLY • link written 4 months ago by Amir.Taheri.Ghahfarokhi • 20

Yes, we are still working on it, thanks!

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, Workflow execution is still an issue. Kindly address the issue at the earliest.

I'm getting the below error.

Successfully invoked workflow Workflow constructed from history 'primary tumor'.

You can check the status of queued jobs and view the resulting data by refreshing the History pane, if this has not already happened automatically.

But I cannot view anything.

Thanks, Jaswanth. P.

ADD REPLY • link written 4 months ago by jaswanth.p • 0

The current status is that Workflows are still problematic and being worked on.

ADD REPLY • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Is this problem solved ? (31.7.18). Because some of my Workflow now work.

Thanks Lorenzo

ADD REPLY • link written 4 months ago by sennalollo • 0

Yes, see the accepted reply above: https://biostar.usegalaxy.org/p/28818/#28950

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Hi, Wonder if anyone can help? I have created a workflow but despite invoking does not appear in the history. It has not been sent to a different history. It appears similar to a problem users had 7 months ago. Wondering how best to resolve this?

Thanks, Josh

ADD REPLY • link written 4 months ago by joshezhang.tfg • 10

Hi Josh - please see the discussion and new issue ticket in the primary reply. We will also post back here with another update once resolved. Thanks for reporting the issue and hope that clears up current status.

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Could you share links to the workflows? There can be multiple version of these on the server and I want to make sure I am looking at the exact version you are using.

I can probably find your originating histories, so you don't need to share them publically. Will write back for more info if needed with how to share privately.

Btw - The Cloudmap workflow and tools are deprecated so that one may not be functional anymore (but a different error message should come up, not a launch with no other information). I'm not sure about the other but will review once I have the link.

Thanks, Jen, Galaxy team

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much for your answer. Today, I tried several times but the problem is still there. I'll keep in touch. Irelka.

ADD REPLY • link written 6 weeks ago by irelka.colina • 20

Thanks again and please follow the updates here: https://biostar.usegalaxy.org/p/28818/#29695

ADD REPLY • link written 6 weeks ago by Jennifer Hillman Jackson ♦ 25k

4 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

UPDATE 7-27-2018

The Workflow execution issues have been resolved at https://usegalaxy.org.

New or existing workflows will execute when the results are sent back to the original history or sent to a new history.

Important note: Prior workflows launched during this problematic time frame had the workflow jobs in a queued state. These are now running or have already run. Be sure to check your histories for this content and permanently delete (purge) any datasets or histories that ended up with duplication (due to multiple invocations of a workflow). FAQ for purging data: https://galaxyproject.org/learn/managing-datasets/#delete-vs-delete-permanently

Thanks to everyone for your patience and feedback while we resolved the problems! Jen, Galaxy team

ADD COMMENT • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k

That's great! Thank you :)

ADD REPLY • link written 4 months ago by jomiles26 • 50

6 weeks ago by

irelka.colina • 20

irelka.colina • 20 wrote:

Workflow delays UPDATE 10-12-2018 (admin edit)

Hi ! I would like if this problem is back, because I'm trying to run a workflow and I get the message to say that datasets have successfully been invoked but the new history is empty. Thanks, Irelka

ADD COMMENT • link written 6 weeks ago by irelka.colina • 20

I can reproduce this for some workflow invocations and not for others (no datasets populated into a new history created by a workflow). We are looking into why.

Meanwhile, try to run the workflow again. It may take a few tries to get one that populates the new history correctly. That should move you forward. If any tool ends quickly with an error stating Specify a dataset of the required format / build for parameter input1. that is another problem we are fixing. Rerunning those jobs will usually produce a successful job -- but that also may take a few tries.

More feedback once this is all sorted out -- it just started yesterday as far as we know. Sorry for the trouble. Recent changes made for the pending 18.09 Galaxy release are likely involved. Thanks for your patience and for reporting the issue. Jen, Galaxy team

ADD REPLY • link written 6 weeks ago by Jennifer Hillman Jackson ♦ 25k

Update 10-15-2018 10:40 am PST

The datasets produced by the workflow will eventually show up in the new history, queue, and execute. This delay is being worked on. Ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/168

Until fixed, please start up the workflow and do not delete the new history created. From testing, the datasets can take anywhere between "immediately" to about "an hour" to display in the new history.

Thanks! Jen, Galaxy team

ADD REPLY • link modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson ♦ 25k

We made some adjustments and the datasets will now display faster. Thanks again for reporting the issue! Jen

ADD REPLY • link written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

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