Error Firecloud joint-discovery-gatk4
Hi, I am running joint-discovery-gatk4 (snapshot 11) on firecloud for 900 TCGA WES samples, and keep on getting the following errors: message: Task JointGenotyping.ImportGVCFs:412:1 failed. Job exit...
View ArticleEndless Abort
Hello, I submitted a job a few days ago and noticed that the tasks were complete, but it was stuck 'Running'. I ran the same job again and it finished in a fraction of the time, so I knew something was...
View ArticleCan you clarify functional differences between Method Repo namespace access...
Method Repository Namespaces have three different access levels: READER, OWNER, NO ACCESS. I am an owner of the broadinstitute_cga namespace. A member of the CGA group here at the Broad recently asked...
View ArticleScatter:Gather by array indices
I have multiple use cases where I'd like to iterate over the indices of multiple same-size arrays (e.g. when aligning paired fastq files or slices of tumor / normal BAMs). Is this something that's...
View ArticleQueued in Cromwell
I'm seeing jobs that are QueuedInCromwell. Is there any way to know when things might start moving through? For what it's worth, on the Monitor tab it says 0 workflows are Queued and 6641 workflows are...
View Articlev100s no longer available on “us-central1-c”
My method uses v100s. It worked perfectly a few days ago. Now FC says it can't find the machine type. What happened to the v100s?
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Job continues to run even if input array is empty
If the input for a workflow is an array of samples and a sample_set is provided (e.g. this. samples.bam) to the workflow but the sample data model table does not contain the mentioned sample attribute...
View ArticleHow to submit "Submission" or workflow using APIs(Documentation too short)
Hi Team, I need your help to guide me as how to trigger submission using APIs. I do understand there is "Create a submission" API as "POST...
View ArticleDocumentation for uploading methods to FireCloud
Hi, I noticed over the weekend that the old FireCloud CLI finally stopped working. I have switched to FISS, but it's documentation is pretty barren. For years I've been able to follow this excellent...
View ArticleSetting / propagating default permissions for FireCloud methods
I've finally got imports working in my FireCloud WDLs (🍾), but updates to a method seem to reset whether it's publicly accessible. Can I set this as a default, or update it from the command line when...
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Cannot delete runaway VMs
Hello, I launched a large number of analyses two weeks ago, and when I looked at the list of VMs I had associated with my billing project, I had 29 VMs that said they were still running associated with...
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Output of workflows not overwriting values in the sample entity
I have a workflow named rna-summarization, and its output is a list of files. Lets call this output 'outputFiles'. After running that workflow, I have another workflow named...
View ArticleUsing gsutil -m: how do I specify multiple sources and multiple destinations
I want to download 15,000 files from my FireCloud bucket, all of which have the same filename but different paths, eg gs://fc-mybucket/MyTool/*/MySubtask/output.vcf It's too slow to make 15,000 calls...
View ArticleIssues with pairsets in absolute
Hello I'm running absolute and having issues with running it on the pairset. I can run it successfully on individual pairs but it fails when it runs on a pairset using this.pairs. I am able to use the...
View ArticleCreate directory command in WDL
Hi! One of the required inputs of my tool is output directory (--outdir), so I'm trying to add a command to create a new directory within my WDL script (mkdir ${outdir}) but it doesn't seem to work....
View ArticleDefining multiple outputs
Hi! My command creates multiple output files and I'm not sure how to properly define them in output section of my WDL script. Here is the script: Rscript ${pcn_extdata}/Coverage.R \ --outdir ${outdir}...
View ArticleQuestions about the very basics, please help
Hi there, I've been trying my best to work through the tutorials, but it's been hard for me to follow. I'd like to do a very simple task just to make sure I understand the parts correctly. Let's say...
View ArticleOauth Authentication for FireCloud via API calls
Hi There, We are integrating our system to fireCloud via APIs(https://api.firecloud.org/). Now to run APIs we need to provide OAuth Token. While testing it via swagger it allows me to log in using...
View ArticleNo machines available error
Hi, I'm trying to interpret the following error: The job was stopped before the command finished. PAPI error code 5. no machines available Does this mean no machines were available from the cloud, or...
View ArticleDeleting Project Data
Hello, I attempted to delete a project and move the data to archival storage-- however my google cloud console activity reports "Failed: Update Bucket" over the many days since I submitted the request....
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