why would a Workflow be marked as Failed?
I am reviewing a workflow. The workflow is marked as Failed (see attached PDF). The workflow ran 3 tasks. Two are done (with green check marks) and one is marked "Running". Of the one that is marked...
View Articlepeek-a-boo error message "Render Failed. See console for details."
After what I think is an update today, every time I go to a method-configuration I see the text "Render Failed. See console for details." in red. Then, about a moment or two later, it goes away (so...
View Articlenumerous docker pull timeouts caused numerous calls to fail
Yesterday I used FC, and I made two submissions. Each submission had a single workflow. EAch workflow had a scatter in it. A number of the "scatter" calls end with something like the following in the...
View ArticleWhat is the status of Job Avoidance (Cromwell Call Caching) in FireCloud?
(@mnoble and his team would also like to know the status) Cromwell has supported Call Caching for some time now. I know enabling it in FireCloud was held off until certain security issues and...
View ArticleWant to be able to edit the documentation of my method after putting it into...
Rather than needing to add it as a completely new method. Not super high priority, just another UI request for the devs.
View Articlebroken link (bug)
If I click on the workflow ID in the monitor section, it should pull up the Google storage console browser window pointing to the workflow outputs from this submission. Currently, doing that leads to...
View ArticleCan you please assemble some user docs for submitting a new method into the...
It's not clear e.g. 1) why I need a Namespace and how it's used, 2) what the Name should be (my name? the method name?), 3) what's the difference between a task and a workflow? (And Kris just told me...
View ArticleSharing not just current version of method config
I am collaborating with someone else on creating new methods for a workspace. Although we have both given each other privileges on the workspace and the relevant methods in the method repo, every time...
View Articleallowing creation of dependant entities from tsv
Hi Firecloud team, I am trying to import samples into my workspace, but before I do this I have to cut out the "participant" column, rename it to "entity:participant_id" and import that first. When I...
View Articledoppelganger/zombie jobs
We launched a number of jobs on Feb 24 that are still running; it is not unexpected for them to take a few days. However, they appear to be getting restarted while the old ones are still running. The...
View ArticleWorkflows are getting stuck in "Submitted"
Last night and this morning (2/28-3/1) when I submitted about 60 workflows, half of them get stuck in the "Submitted" stage. The other half run to completion.
View Articlefailed workflows due to an Agora failure?
On 2/11 at around 10:30 AM I submitted an analysis that launched 1000 simple, single-task, workflows. 179 of these failed immediately with the following error: ErrorReport(rawls,Unable to query the...
View Articletask is marked as "Starting" but it is done and its output is used by...
I have a submission where the first task is "calcDiskSizes". It is the first task in the WDL. It's output is used to specify disk sizes for downstream tasks. In the UI the task is 1) marked "Starting",...
View Articleteam permissions for methods
We are running into issues with the method repo security model. The GDAC team wants to be able collaborate on a set of methods. Methods pushed to the method repo by any of the members should all be...
View ArticleHow does one load ~10k TCGA participants, samples,pairs, and pair_sets into a...
Hi I'm trying to load the bulk of TCGA data into a workspace using the "Import Data" dialog box. Is there a way to add all entitites to the target workspace without having to click on each one? I could...
View Articlekilling portion of submisson?
Is it possible to kill a portion of a submission? We re-launched the remaining 19 REBC jobs on non-preemptible 64 core VMs. Of these, 3 failed instantly; we have relaunched them. Also, 2 others appear...
View Articletransient workflow failure
A submission made March 10, 2017, 5:14 PM, containing 19 entities in its pairset, had 3 of them fail within minutes. While it was easier to mitigate because the problem 1) occurred quickly and 2) was...
View ArticleNon-preemptable jobs spontaneously restarted
Submission ID 9dc58cc3-b495-4c61-be5a-28254e180ac8 was started on March 2nd (MutTect2 jobs on 24 REBC pairs) with preemptable=0. We previously commented that these jobs took many hours to actually...
View ArticleJob is done but Cromwell thinks it is still running?
In the UI I see that a job started last night (around 5:19PM) is apparently still running this morning (~9:00AM) : Call #15: ID:operations/EJbDvOimKxiPoePtu4iSrLUBIN6K28SDHCoPcHJvZHVjdGlvblF1ZXVl...
View Articleorphaned operation ID, in the context of timeout....is it a known issue?
@khal consider this operation ID operations/EPe8-cr_KhjGluSduevM0Xcg_eDe0bUCKg9wcm9kdWN0aW9uUXVldWU I find its exec.sh to find the workspace ID, submission ID, and workflow ID : wm8b1-75c:script...
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