Workflow failure dependent on FireCloud Billing Account?
I have two identical workflows (broad-firecloud-ibmwatson/CBB_20181127_CGA_WES_Characterization_TCGAControlledAccess_test and...
View ArticleMark Duplicates extremely slow in particular settings
Hi, I have about 200 subjects that I would like to run through the gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl workflow. However, when arriving at the MarkDuplicates step the...
View ArticleWorkflow failure dependent on FireCloud Billing Account?
I have two identical workflows (broad-firecloud-ibmwatson/CBB_20181127_CGA_WES_Characterization_TCGAControlledAccess_test and...
View ArticleMutect 2 on mouse cells
Hi, I am hoping to run Somatic-SNVs-Indels-GATK4 on whole exomes from a paired mouse cell lines. Just wondering where can I find the relevant intervals and reference files for this? Thanks!
View ArticleRunning costs on FireCloud
Hi, I'm trying to find out about how much it might cost to run a cohort of samples (500, 1000, or 2000) using germline GATK Best Practices Pipeline on FireCloud , and also how long the runs might take....
View ArticleWhat is the plain text for an Array in Workspace Attributes
What is the plain text for an Array in Workspace Attributes? If not exist, how can I upload an array in my workspace attributes? Say I want to copy the "known_indels_array" attribute in the following...
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 ArticleWorkFlow getting aborted intermittently without any exception
Hi Team, We are facing yet another issue with the large file(68GB) processing wherein workflow is getting aborted all of sudden without any exception on AWS enabled Cromwell. This behaviour is not...
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View VMs associated with running jobs in GCP
I am trying to view my jobs in GCP. For the free trial account, I do not have have any active jobs in my job history but I do have a VM running in GCP. It's been running since 4/17. See screenshot For...
View ArticleDocker pull error
I am getting the following docker pull error when working in a project that is using my google billing account instead of the free billing account. Task genoml.train:NA:1 failed. The job was stopped...
View ArticleCan I add the hash of docker container to my snapshot?
runtime { docker: "imagename":HASH memory: memGB disks: "local-disk 256 HDD" cpu: nCores } This would be useful for forcing versioning of the docker image in the snapshot.
View ArticleConfirm I am getting the right runtime and runtime options
How do I confirm that I am getting the right runtime and where are the different WDL runtime parameters/options described?
View ArticleImplementing GenotyGVCFs and GenomicsDBImport in WDL
This discussion was created from comments split from: Picard/GATK MergeVcfs throws errors.
View ArticlePlink prefix and wdl
Hi, I am trying to create a WDL that runs plink and takes as an input a prefix to the bed/bim/fam file I am using Cromwell and docker to run it for example: plink -bfile prefix --recode --out prefix...
View ArticleHow to exit in the middle of a linear chain tasks in wdl
Hi, I have a sequential of tasks. If I found the output of task1 has an error message "No space on the disk", I would like to exit the analysis. Don't continue with the following tasks. Is that...
View ArticleFailure while processing large unmapped bam file as input to cromwell
Hi Team, We are running five dollar pipeline by running Cromwell(v39) on AWS. Whenever we are running our pipeline on small files(~300MB) process is proceeding fine with further processing. But,...
View ArticleHow to change billing account/billing project initially assigned to a workspace?
Hi, Could you please let me know how can I change a billing account/billing project that I initially assigned during generation of a workspace in Firecloud?
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Error uploading samples table to workspace
I get the following when trying to upload a 7mb table to my workspace. Is it too large?
View ArticleIs Terra/Firecloud down?
I can't login. Get a gcp error. "502. That’s an error. The server encountered a temporary error and could not complete your request. Please try again in 30 seconds. That’s all we know."
View ArticleDoes the notebook cluster showdown if you logout of Terra?
I ran an ML job on the notebook cluster which was running fine but overnight. When I came back in the morning the cluster had shutdown and my job was killed. Is that the right behavior? Thanks, Ilya
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