Need better error message on adding users to groups
I tried adding a user who isn't registered yet to one of my FireCloud groups and got this error message (with the name changed so I can post it in public): Error: Sam call to HttpMethod(PUT)...
View ArticleDownload WDL and inputs.json from Firecloud
Hi, I'd like to download a project from Firecloud and run it locally: https://portal.firecloud.org/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-b37 Is there a way to download the whole WDL +...
View ArticleFireCloud -- hard to understand failure (parameter.name too long)
My FC method is failing with an inscrutable error: Invalid value for field "parameter.name": too long: 132 bytes, want no longer than 128 bytes Is this 128 byte limit something universal that I'm...
View ArticleChange billing account
Is it possible to change the billing account for an existing FireCloud project? Thanks.
View ArticleUnable to view failed workflow.
I ran the mutect2_pon workflow (a GATK best practice workflow) for creating a mutect2 panel of normals. I ran the workflow on a set of normal samples from the TCGA THCA cohort. The workflow failed....
View Articlesamtools view slice of cloud storage bam not working
Hi, I am working with WGS data, and since it's so huge (upwards of 300 GB in some cases), when I scatter across many instances I'd like to be able to avoid localizing the entire bam for each scatter....
View ArticleCromwell WDL not working in FireCloud
We have a fairly complicated WDL that we are trying to run in FireCloud. It works locally, but is failing after submission in FireCloud and we can not figure out the problem. Method Repository:...
View ArticleSpecify minCpuPlatform in Firecloud?
Hi, I was handed a WDL that specifies the parameter "minCpuPlatform" in the runtime section. This appears to correspond to the google cloud platform's "CPU platform" dropdown:...
View ArticleIssues with adding method config annotations
Hello, A colleague and noticed that when we were trying to add or delete intermediate characters in a method config annotation, we would get pushed to the end of the string after adding or deleting a...
View ArticleError when trying to share workspace with user or add to user group
I'm trying to add a Broad account to a user group and am getting a very strange error: Database error: email yanay@broadinstitute.org refers to too many subjects The same thing happens if I try to...
View ArticleCredential error early in pipeline run
Hi there, I'm trying to run the cellranger pipeline and got the following error very early in the run: "cannot find credentials for...
View ArticleWhat is the fastest way to
Someone has given me access to a method and method configuration. I have a slightly updated WDL that I would like to use in my own private workspace. The method configuration is big and I do not wish...
View ArticleUnclear error: PAPI error code 10. Message: 14: VM ggp-14729985031179362160...
When I was running one my workflow in aryee-merkin/dna-methylation-pipeline-paper I got this error message: Task call_bismark_pool.merge_replicates:NA:1 failed. The job was stopped before the command...
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Error Loading Workspace Info When Underlying Bucket Does Not Exist
Someone recently shared a workspace with me so I could look at their method configs and workflows they had run but it seems like they have also deleted their underlying workspace bucket (or something...
View ArticleAre the links in email notifications unable to handle spaces in workspace names?
Dear FireCloud user, David Benjamin has given you OWNER access to the following workspace: https://portal.firecloud.org/#workspaces/broad-firecloud-dsde/Mutect2 WDL testing This link above is broken in...
View ArticleGATK mutect2 failing on gnomad input size determinatino
Hi, I am running GATK's mutect2 on FireCloud. I am using the value "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf" for the attribute gnomad. I am receiving this failure message:...
View ArticleWDL size function for Array of files
How would I use dynamic sizing for an array of files? The documentation only specifies the answer for a single file: https://software.broadinstitute.org/wdl/documentation/spec#float-sizefile-string...
View ArticleCNVSomaticPairWorkflow DenoiseReadCountsNormal PoN Error
Hi, I'm running the CNVSomaticPair Workflow, and am using the gatk-recommended WGS panel of normals "cnv_somatic_PoN_4.0_WGS_for_public.pon.hdf5" which I found in the bucket...
View ArticlePAPI error code 10. Message: 14: VM ggp-17100430892766313741 stopped...
Hi, I launched a simple trimming and fastqc WDL to google cloud for processing, but I am always seeing failing messages similar to below. The WDL run fine locally and I have tried running 1 sample...
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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