Orphaned VMs
I have two VMs that are still running despite all jobs having completed or aborted. The console shows a cromwell-workflow-id for each VM -- is this the same as the workflow ID in FireCloud? I couldn't...
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Error message: Lock wait timeout exceeded
Some of my workflows have been failing with the following error message this afternoon: I'm happy to restart them to see if they'll just work on a second attempt, but some of the workflows are still...
View ArticleFeature request: Relaunch failed workflows
Sometimes workflows fail with benign errors and just need to be relaunched. Currently if 20 out of my set of 50 workflows failed I can either: Launch 20 individual workflows, Create a new set of 20...
View ArticleTotal Run Cost doesn't show up in my workspace
I see that Total Run Cost is added as a new feature for firecloud jobs. Most other workspaces that I work with shows the run cost after a day or two. But it still says not available in the workspace...
View ArticleFirecloud isn't submitting workflows?
Currently, when I click launch I just see a spinning wheel with "Launching analysis ...". Then eventually it seems to time out and it stays on the Launch Analysis page and doesn't appear to actually...
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Successful jobs marked as failed with "java.net.SocketException: Too many...
Hundreds of my jobs "failed" with this error. Example: workflow ID: afefd9d6-d9c0-459a-9d95-625c260cac44 submission ID: eef7d920-d17f-44b2-929d-91b42d6b18d5
View Articlevendor pre-built reference package
Hi, firecloud team I am aligning my WGS with vendor pre-built hg38 reference package, which contains decoy contigs, but not alternate haplotypes and MHC alleles, compared to standard hg38 reference...
View ArticleError in creating new billing project: 429, too many requests
I am attempting to create a new billing project in FireCloud and received this error: Insufficient tokens for quota 'servicemanagement.googleapis.com/default_requests' and limit...
View ArticleIssue with Mutect2
Hi, Firecloud team I've tried Mutect2 for some times recently on my WGS data, but they all failed. I know some of the early failure are associated with some old scripts, but now I change to most...
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BUG: getEntitiesWithType API broken
I first got this error with FISS, but on trying to troubleshoot via the swagger documentation at api.firecloud.org, I found it persisted: returns: { "statusCode": 500, "source": "FireCloud",...
View ArticleTransient error
I got the following error on one shard of my workflow: Task CallManySamples.M2:43:1 failed. The job was stopped before the command finished. PAPI error code 5. Message: 8: Failed to pull image...
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Firecloud status banner is now grey
The firecloud status banner has recently changed colors from red to grey, which has very little contrast to the background colors and is very hard to notice now. Would it be possible to switch back to...
View ArticleQueued in Cromwell
The workflow I'm currently running seems sluggish this morning. Some tasks say Queued in Cromwell and some jobs are taking 20 minutes to realize its a call-cache hit. I'm wondering if others are...
View ArticleUploading an Array of files or strings - WDL won't overwrite data model
Hi- Many of my methods rely on arrays of files as inputs from the data model. Normally, I use this wdl to populate the data model: task read { File list command { ls } runtime { docker:...
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Method Configuration Versioning within Workspace
Hi Firecloud Team, When I am am working within a workspace and import a method configuration, I can launch a job from that configuration, but when I go to the monitor tab, I cant seem to figure out how...
View ArticleExited with return code 1 which has not been declared as a valid return code.
Hi all, I am trying to debug a workflow that failed to run on Firecloud. I am getting an error message which I don't understand: message: Job captureWorkflowSNVs.Gather_mutect_Task:NA:1 exited with...
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Total Run Cost estimator...
Hi Have there been unexpected delays in estimating Total Run Cost for a job? The little (i) info button suggests to wait for a day or so after a job completes, but jobs that finished a week ago appear...
View ArticleIssues with accessing notebook cluster
I have been getting a lot of these messages today when trying to access my notebook cluster (broad-dsde-firecloud/validation): The server was not able to produce a timely response to your request....
View ArticleUnclear error in Fire-dollar-genome workflow
Hi all, We run the five-dollar-genome and then we got an error about failing to transfer file. It is not clear why? and how to solve it. You can see the error message we received. message: Task...
View Articlefuncotator error
Hi, FireCloud team I ran into a problem recently coming from Funcotator. I initially run Mutect2 coupled with Funcotator on FireCloud, GATK 4.0.4.0 version (my data is aligned with hg38), but it throw...
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