Notebooks authorization error
Hi- My group is having some trouble authorizing a user to create clusters through the Notebooks tab in Firecloud. We are getting the error: Error: ‘m**a@broadinstitute.org’ is unauthorized Hide Details...
View ArticleWhat differences between MergeVcfs and CombineGVCFs?
I read a workflow , is it just able to combine vcfs from different intervals ?
View ArticleWill the Cromwell upgrade on 11/1/2018 2:30 - 3:30 pm EST kill jobs?
Will the current Cromwell upgrade interrupt or disrupt jobs that are currently running?
View ArticleUnable to launch jobs
Hi team, I am not sure if this is being observed by other users but I cannot launch methods in FireCloud. The following error is returned Error: Lock wait timeout exceeded; try restarting transaction...
View ArticleClik here to view.
How do I authenticate to the API?
I hope this isn't a stupid question, but after reviewing the Swagger documentation and studying the API calls occurring through normal usage of the FireCloud web app, I'm ready to do start using the...
View ArticleJob exited without an error, exit code 0. PAPI error code 5. 10: Failed to...
Hi, I'm trying to uncompress some files using Firecloud. I get this error: Task helloUncompressGZ.UncompressGZ:NA:1 failed. Job exited without an error, exit code 0. PAPI error code 5. 10: Failed to...
View ArticleClik here to view.
can this workflow work?
these days ,i have been doing call snp with my multiple samples` RNA-seq data , and i read two workflow:A and B so i got some questions below: 1.i want use workflow B to call snp for my every single...
View ArticleCan't run mop using fiss
I'm getting the following memoryview error, seems like there is a bug here?: fissfc mop -w DNA_RNA_Mutation_Lung -p vanallen-firecloud-dfci WARNING: Delete 1138 files in...
View ArticleAdd GATK3 Variant Refinement
I note that the GATK 4 pipelines have a joint_discovery workflow, e.g. the gatk-workflows/gatk4-germline-snps-indels repo. However, this doesn't exist for the GATK 3 pipelines:...
View ArticleTasks queued in Cromwell
I have about 100 workflows with tasks that are queued in Cromwell. Workspace is broad-firecloud-ibmwatson/IBM_Wagle_Analysis. Submission ID is e2a862bd-a879-4174-bb77-f6616e7aa67d.
View Articlerunning cromwell with google cloud call VM with external IP address
Hi, I tried running the five dollar pipeline with WGS on google cloud and saw that it is always creating VM instances with external IP. Is there a way in cromwell runtime to control the VM instance...
View Articlecan't post any more due to "links"
Hello, I was able to ask a detailed question with links previously, but now I get the "you have to be around longer to post links" message. Can someone verify me so I can resume posting? Thanks Joe PS...
View Articlebilling project setup issue
I created a new billing project hailbp linked to account Broad Institute - 5216186 The circle appeared and spun for several moments and then timed out. Upon refresh, the billing account did not show...
View ArticleClik here to view.
Lost connection errors
Hello, 18/1000 of my tasks in a batch failed, all of them providing the error attached in the first screenshot. While frustrating, my inclination would be to try running these samples again later....
View ArticlePossible bug in construction of web links to google buckets
I noticed in a recent job:...
View Articlebug report: Sign in with Google on Chrome doesn't work
I'm seeing the following behavior on Google Chrome: - Go to the FireCloud portal (portal dot firecloud dot org) - See the New User?/login landing page - Click "Sign in With Google" - Get a pop-up to...
View ArticleWhat is running?
I have several workflows that have the status "Running", but I don't see any active jobs. How do I figure out what is running (e.g....
View ArticlePurity adjustments for CNV calls from the GATK-CNV Firecloud pipeline
Hi Firecloud/GATK team! We are really enjoying using the CNV pipeline in Firecloud - so far it's giving us some of the cleanest calls we've seen and the "extras" (like figures, baf, etc.) are all...
View Article