Running the firecloud API from a google compute instance
I have been trying to run the firecloud api tools (fiss) from my google cloud instance and have been running into some issues regarding authorization. When I do the same steps on my local computer...
View ArticleService account is not registering
I have submitted the following command to register a service account: docker run --rm -it -v "$HOME"/.config:/.config -v /Users/sbryant/bench:/bench broadinstitute/firecloud-tools python...
View ArticleHow to remove unwanted data from my workspaces?
Does portal.firecloud have this option?
View ArticleThe Google bucket associated with this workspace is currently unavailable
Hi, I'm unable to access the google bucket associated with ccdg-freeze2-supp/CCDG_Freeze2_External_Crams through the Firecloud UI. Other members of my team have been able to do so, but this has not...
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Notebooks - Cluster absent from list
Hi - I'm working with Hail through jupyter notebooks in Firecloud. I've come across what seems to be a bug. After going through the setup for a cluster and clicking "Create", I was returned to the...
View Articleworkflow: SingleWorkflowRunnerActor workflow finished with status 'Failed'.
i am running the example workflow locally following instrctions here: https://gatkforums.broadinstitute.org/gatk/discussion/12521/how-to-execute-workflows-from-the-gatk-workflows-git-organization I got...
View ArticleWhat is the limit on the jobs that can be launched while analyzing a large...
Hello, I am analyzing a data set that has 78,000 samples where my method runs five serial tasks on a MAF (i.e. no scattering). As of now I am running my analysis task in batches where I do not run the...
View ArticleCalling non-public sub-wdls?
What is the best practice for calling non-public sub-wdls, since importing a non-public WDL using the FireCloud API (e.g....
View Articlestdout and stderr are not supported in preview
Hi, I'm using firecloud, and all my calls generate a stdout and stderr file. It would be a nice feature to have if you could click on either of these files and view their contents. At the moment I get:...
View ArticleWhat is meant by firecloud.org can manage my Google Compute Engine resources
I just logged into FireCloud using my personal gmail account (I had previously registered with FireCloud under that account). Since it had been some time since I had last accessed FireCloud under that...
View ArticleMultiple issues with FC workflow execution & call caching
Hi FC team, Our team has been unable to get any workflows to successfully complete since mid-afternoon yesterday, Tues, Oct 2. We have experienced these issues across multiple workspaces, workflows,...
View ArticleDocumentation for uploading data
It used to be that when you went to upload a data file there would be a link to documentation (see attached screenshot). The user guide link used to take you to documentation about how to upload data...
View Articlelong wait times
Hi Earlier today I submitted a job that would normally take an hour or so but today seems to be taking much longer to get into a running state. Does the message at the upper right on the monitor page:...
View Article2 hours per task to check call cache
In my run at https://portal.firecloud.org/#workspaces/regev-development/ATAC-Seq/monitor/7635ab80-5237-42e7-9a2d-fd3c9fd9e248/3483bf20-abcb-4d13-a2eb-7f9c616efa14, FireCloud is taking around 2 hours...
View ArticleCreate a FireCloud Billing project, that links to an existing GCP project?
Hi, I recently created a new billing project on Firecloud (linked to GCP billing account) but how can I create a FireCloud Billing project, that links to an existing GCP project? Thanks, Lily
View ArticleExplanation of workflow timing
In my workflow timing diagram I see "RunningJob" before "pulling-image"-what does running job actually mean? After "pulling-image", I see "ok"-what does "ok" mean? Lastly, I see...
View Articleregarding hail 0.2 in firecloud
I am trying to run hail 0.2 in fire-cloud , can someone tell me how to run ? as i can see an inpt format particluar to hail 0.2 in my google bucket so want to ask how to do it?
View ArticlePermission to upload and delete files in google bucket
Hi, I used to be able to upload and delete files in my google bucket, but recently there seems to have been a change in user permissions, and now I am no longer able to upload/delete files from my...
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No status update in the monitor tab
I launched a workflow ~20min ago but there isn't anything listed in the monitor page such as called tasks and workflow log. Is my workflow running, do i need to relaunch the workflow? The queue doesn't...
View Article50 submissions stuck in status "QueuedInCromwell" for over an hour
I have 50 submissions that I made over an hour ago that still don't seem to be running. The Workflow Timing diagrams are empty, and the call status is "QueuedInCromwell"....
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