PoN for CNV_Somatic_Pair_Workflow
I am looking to use the open access PoN (gs://firecloud-tcga-open-access/tutorial/reference/open_access_pon_from_1000g.pon) but when I use this file as the input into the method I get the following...
View ArticleLockout errors appearing when calling tasks and uploading metadata
Hello, I am writing to report that I have experienced periods this morning and later afternoon where I have attempted to run a workflow in Firecloud but when I press launch, I get a long loading...
View ArticleSignificant slow down of Firecloud
Hello FIrecloud team, Since the latest release I see significant slowing down of Firecloud. It takes around 16-17 seconds to just load method configuration in the workspace and then another 20 seconds...
View ArticleThe Google bucket associated with this workspace is currently unavailable.
Hello there, I've been trying to download data from the following workspace: regev-collab/180627_NB501583_0384_AH3LK3BGX7 It's been a couple hours that I've been getting the following error: "The...
View Articlefive-dollar-genome-analysis-pipeline running errors in CheckContamination
I have cloned the five dollar genome analysis pipeline and uploaded my own WGS input data, however, I encountered problems in CheckContamination stages: Job...
View ArticleFireCloud Methods: Bam->uBam, uBam->realigned Bam
This discussion was created from comments split from: Realignment (reference liftover) workflow or service in FireCloud.
View ArticleUnable to view samples or run sample level analyses
I have uploaded several samples and pairs referencing these samples to my FireCloud workspace. When I try to click on the samples tab in data, I am led to a completely blank screen. This also happens...
View Article[GATK4] Mutect2 unable to evaluate gnomad_vcf_size
Hello, I'm currently trying to run the "mutect2-gatk4" public method (snapshot ID 12), and I'm hitting the following error: message: Failed to evaluate 'Mutect2.gnomad_vcf_size' (reason 1 of 1):...
View ArticleTasks stalled at "Queued in Cromwell" status
Hello, In the last hour and a half, I have been unable to get tasks running in any of my workspaces. The workflow is launched and in "running" status but the calls are stuck in the "Queued in Cromwell"...
View ArticleBug report: Estimated Monthly Storage Fee does not take storage class into...
For example, if I change all the objects in a FireCloud bucket to be coldline storage the estimate is off by a factor of 3.5. Thanks.
View ArticleCapture user that ran workflow
I noticed that FireCloud/Cromwell adds a GCP label in order to track costs by WDL task name (wdl-task-name) which is great. However, we have many users that share the same billing account. Is it...
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Getting error when uploading the genomic data model
Hi FireCloud team, I am getting this error when trying to upload my data model. I don't have any duplication! Can you please help? Best,
View ArticleError running "gatk/mutect2-gatk4"
@bshifaw @Tiffany_at_Broad @KateN, Thanks a lot for your helps. I'm almost finished this analysis. When I run mutect2 on the normal-tumor pair, I encountered this error for call #50 of Mutect2.M2:...
View ArticleUpdating entity attributes - Lock wait timeout exceeded
I'm trying to update entity attributes via the workspaces/{namespace}/{workspace}/entities/batchUpdate URI but I keep getting "Lock wait timeout exceeded" errors. The first time I tried, the response...
View ArticleAccessing external web services disabled?
I have a task that up until recently worked fine. Now I get the following error: Could not find annotation file Get...
View ArticleFirecloud office hours
Hello, I was wondering if there are office hours for Firecloud questions. Thank you.
View ArticleNotebooks have stopped working?
After yesterday's outage it looks like my notebooks have "Stopped". It would be really fantastic if there was a way to get the scripts that I had written back (which were sitting on those VMs). I can't...
View ArticleSample Tab in Data Model leads to blank page.
This has happened to a couple of Workspaces, but varies from user to user. If we click on the samples tab of the Data model, we are sent to a blank page. The URL seems correct, and ends in /data but...
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IGV on FireCloud Analysis Tab
Hi, Great workshop today in Cambridge, thanks guys! Just a quick q... Is it possible to change the reference genome/species used for the IGV.js embedded viewer on the Analysis tab please? Great tool to...
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