seeking a full enumeration of workflow submission states
What is the set of possible states returned by the listSubmissions API ? To date we've observed that the workflowStatuses field can have these values 'Succeeded' 'Failed' 'Running' 'NotRun' but surmise...
View ArticleFirecloud office hours
Hello, I was wondering if there are office hours for Firecloud questions. Thank you.
View ArticleJupyter notebook examples
Hi The Jupyter notebook tutorial at https://software.broadinstitute.org/firecloud/documentation/article?id=11603 suggests that users can explore and play with some example notebooks at link:...
View ArticleIs there a way to get the execution time for workflows that ran as a batch?
One of my method configurations has participant as the root entity type but I have ran it with a participant- set with hundreds of files. Is there an easy way to obtain how long it took to finish the...
View ArticleCleaning Failed Runs / Temporary Data
Hi All- Curious if there is a straightforward way to trim away failed runs and temporary files in FireCloud once we are satisfied with the output on a method run level? The storage costs proliferate...
View ArticleEasily clone a method config from UI
I searched the forum for "clone method config" and "duplicate method config" and "copy method config" but came up empty. So, here's a use case for the UI: would be nice to have a Clone button on the...
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Duplicate accounts in permissions for a FireCloud workspace
Last night around 8:27 PM (Eastern Time 2018-04-03), a Single Cell Portal (SCP) user encountered an error when trying to access their study page due to a FireCloud outage. This happens here and there....
View ArticleHow to share a configuration with cooperaters?
I can share a method by add a new user in the permission list. But, I also want to share the configuration. Thanks!
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FireCloud creates non-preemptible VMs for a preemtible workflow, racking up...
Hi FireCloud Team, I noticed a $308 charge for ~6000 hours of compute time on a "standard" (non-preemptible) VCPU, while the workflow I'm running is preemptible and designed to shut off after 24 hours....
View ArticleSetting up an institutional account
I would like to start working in the FireCloud environment and was able to create a "personal" billing account and access the service to try it out. To establish an institutional account, I followed...
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Workflows hanging, stuck on "Aborting"
Hi- I'm having some issues with workflows hanging prior to launching any tasks. I've also noticed that even if I abort, they stick with the status "Aborting" indefinitely. This problem has appeared...
View ArticleRealignment (reference liftover) workflow or service in FireCloud
Hello, I was wondering if a workflow / service exists on FireCloud for realigning BAMs (aligned to a non-standard reference) to the Broad’s hg19 reference. I recognize that a WDL exists for realignment...
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Bug: Queued in Cromwell
At about 7:00 pm EST last night, jobs submitted to FireCloud have been stuck in Cromwell Queue. There is another thread about this but it has an Accepted Answer associated with it, so I am not sure if...
View ArticleFeature Request: built-in cost reporting
I've been using the cost reporting script in https://github.com/broadinstitute/firecloud-tools/tree/master/scripts/bigquery_billing_report. It would be fantastic if FireCloud could automatically...
View ArticleNo stdout produced from job
Hello, I am running a task on a sample set, and while it succeeds for some (often the majority), there are several samples that fail with the following message: "OSError: [Errno 20] Not a directory:...
View ArticleMonitor claims "Call caching: Disabled" erroneously
In the first few seconds of a submission (before it actually gets going) the Monitor will state that a certain submission has Call Caching disabled even though this isn't true. A frantic refresh will...
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Error Message: The job was aborted from outside Cromwell
I have a job that I believe has run out of memory. However, there is not a helpful error message for that task. Sometimes the stderr has the beginning of what I'd expect, but then suddenly stops in the...
View ArticleIs there a simple way to regenerate the directory structure of scattered files?
It's a common paradigm for tools to expect files to be organized in a certain way. Is there a simple way to preserve the initial organization of files? E.g. They are loaded in a directory in the...
View ArticleRawls failure in 10 of 402 workflows launched in single submission.
I launched a complex workflow (a version of CGA's production analysis workflow) on 402 sample pairs. 392 of the workflows successfully launched and completed, 10 of the workflows failed to launch, with...
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