Can you provide a detailed explanation of workflow timing diagram?
Looking at the workflow diagram, I see for each call a multi-colored bar describing the changing state of a job (called task) on FireCloud. The GUI makes it difficult to get information on each of the...
View Articlemissing error message for workflows? missing from workflow log? missing from UI?
I made and ran workflows. The workflows failed. I'm pretty sure that one of the workflows failed because the file referenced does not exist. If I go to the workflow input and click "Show" and click on...
View ArticleFirecloud UI error messages
Testing a wdl in Firecloud (after it validated with wdltools) it failed quickly, but there was no output in stderr, stdout, or the Jes log. I spent a couple of hours trying different tweaks to see if I...
View ArticleHow can I tell if my jobs were preempted?
I'd like to use preemptible VM instances for some of my jobs. After a submission is completed, how can I determine the jobs that got preempted, and the number of times they were prevented (can get...
View ArticleWhy am I seeing no evidence of preemption?
I am running tests using a workflow (somatic mutation calling) which includes the 25-way scattering of a mutect1 job. The workflow is configured to run those scatter jobs on preemptible VMs. We have...
View Articlegoogle JES/backend running but not running? is it running or not?
I ran a submission on FireCloud. Submission ID 61517c58-7cb4-4e53-a782-9b31b3359136 In that submission I have a task that seems to be running but not running. More specifically I refer to task...
View Articlesample set size viewing (in?)ability
@Geraldine_VdAuwera @mnoble A concern has been expressed about the ability (inability?) to see sample set sizes in the data tab. If I go to a sample set I am able to see the sample set size. To help...
View Articleconnect timed out
Today I made a submission of a single data entity (pair). And got a "connect timed out" message. I immediately resubmitted and the error was not observed the second time. It would seem that since the...
View ArticleFireCloud Cromwell incorrectly instructing JES to run task on preemptible VM
As mentioned on two other forum threads (see http://gatkforums.broadinstitute.org/firecloud/discussion/8832/how-can-i-tell-if-my-jobs-were-preempted and...
View Articleempty error?
I view a log file and its preview. I get a message that says "Error! See details below" But if I click "Show full error response" there is seemingly no message is this desired behavior?
View Articleworkflow(WF) running in controlled access(CA) workspace fail if CA turned off...
Tuesday had I relinked my FC account with my dbGAP access. After the successful link I was able to enter some controlled access workspaces and launch a workflow. For example, I entered a workspace and...
View Articleseemingly whimsical dbGAP linkage causes workflow failures?
my dbGAP access has seemingly been whimsical. Going out unexpectedly. See also...
View ArticleData with newlines and tabs
I have data that contains newlines and tabs and and when I "download sample data" from the GUI I get an unusable file. it would be good if there was an option to export to excel perhaps, or to...
View ArticleAnalysis Submissions stalled at start.
Any submission we make now make does not run. We have tried this in multiple workspaces. THIS IS A BLOCKER FOR OUR WORK Here is just one example I submitted an analysis in the workspace...
View ArticleConnection attempt to cromwell2.dsde-prod.broadinstitute.org:443 failed
I observed this message on FC today . Is this a known issue? Is FC undergoing maintenance today?
View Articlecertificate on portal.firecloud.org has expired
When you go to portal.firecloud.org, the browser reports it is unable to validate the certificate. Chrome reports the connection is not private, Safari reports it cannot verify the identify of the...
View ArticleRead Timed Out : Failed to upload authentication file
I tried to run a WDL and after seeing no error in the UI, I found the following by inspection in the network tab of the developer tools of chrome: "submission": "2017-02-02T21:20:36.546Z", "status":...
View Articleissue with size arithmetic in FC
I have a task in a WDL with a variable "diskGB" that is defined as Int and is used in the local-disk runtime setting like so : task token_make { File refTar File bam File bamIdx Int diskGB ......
View ArticleMoving docker disk image off boot disk?
Is it possible to move the Docker disk image files off the boot disk? In Cromwell 19.3, two different disk size parameters need to be set in the runtime block of the wdl, eg via the following: disks:...
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