message: Unexpected failure in EJEA. (again)
Hi Firecloud team, I saw that a few weeks ago there was a post about a similar error. I tried to run a test workflow that previously worked yesterday, and got this error. message: Unexpected failure in...
View ArticleCannot log into forum
Hi Firecloud team, I tried to log in with my google account, but got 400 error:redirect_uri_mismatch I had to create this temporary account to report this. I tried on two computers and had the same...
View ArticleCannot find or see tutorial or shared workspaces in firecloud
Hello, Since I have gained access to FireCloud, I have been unable to see any workspaces on FireCloud, including the tutorial workflows. In what I think may be a related issue, I am also unable to...
View ArticleAn array of files as an entity attribute in data model
I didn't see this in the documentation, but I might have missed it. Is it possible to specify an array of files as a data model entity attribute? I have a genetics data set, with participants and...
View ArticleUpload of partial pair metadata
I found that when uploading a pair meta-data file that all association columns (participant id, case sample, control sample) are required. Are we not allowed to do partial updates of data? e.g. add a...
View ArticleWhat is the status of file streaming?
File copying is still an issue, and there was some discussion about allowing signed urls, or some other method of allowing random file access without copying the entire bam in. (a lot of downstream...
View ArticleJob stuck in the running state
My workflow (attached) ran and has a job stuck in the running state. The first task, bsmap ran and succeeded (the job outputs are in the appropriate google buckets) and status is properly...
View ArticleRFE: RESTful api needs a workspace rename feature
I am currently not seeing such at https://api.firecloud.org/#/Workspaces Thank you, Mike
View ArticleCryptic error message in Firecloud job execution
Hello, I am running the method configuration "ebert-pipeline2" from my workspace "ebert-pipeline-test". When I begin running the pipeline on a sample, Firecloud can copy the files correctly and begin...
View ArticleCannot access hg38 open access workspaces in FireCloud Data Library
We created open and controlled access workspaces for each of the hg38-harmonized TCGA cohorts (cancer types). The controlled access workspaces are in the TCGA-dbGaP-authorized authorization domain, the...
View ArticleNeed info on how to create a sample_set in the FireCloud Basics section
I was a bit lost in the Methods Configuration section, specifically under the "Workflow Expansion Expressions" subsection. I want to be able to run my workflow on each of the samples in a sample_set,...
View ArticleJuly 19th release has broken GDC file retrieval
We run workflows to download files from the GDC and copy them into cloud storage. The two workflows are: broadinstitute_cga/gdc_file_downloader/1 broadinstitute_cga/gdc_bam_downloader/1 The workflows...
View ArticleError recreating a previously deleted method
In Method Repository, I created a method GenomeStrip/RunScript, but then at some point I accidentally redacted it. However, when I try to create another incarnation of GenomeStrip/RunScript, I get the...
View ArticleMismatched statuses getting worse
Hi Firecloud team, I've encountered this bug across two different billing projects over the last two days, every time I run a job with ~200 submissions. When in the monitor tab, When I look at the...
View ArticleData model not updated
Hi Firecloud team, Is this a regression, a bug, or not intended functionality: I am trying to run a workflow, but I don't want to write all outputs to annotations because it clutters the workspace....
View ArticleRunning jobs not terminated when workflow is aborted, incurring cost
Hi Firecloud Team, I terminated a submission in Firecloud (~100 workflows, 88 were running) The workflow is marked as "Aborted" in Firecloud, but the VMs were not terminated (88 are still marked as...
View ArticleWorkspace clones & inheriting permissions
Hi, As best I can tell, workspace clones don't appear to inherit permissions (in my case, read permissions) from the original parent workspace. Is this correct? If so, is this intentional? It seems...
View ArticleAny way to download hellbender-all-1.0.jar?
Hi, I'm trying to reproduce some Firecloud best practice workflows locally. However, some files used in the workflows could not be downloaded. For example, /usr/local/bin/hellbender-all-1.0.jar was...
View ArticleMore retries than preemptible setting?
I'm having trouble interpreting one of my timing diagrams. One of my workflows seems to have retried more times than my preemptible setting (which was 3). Granted the task...
View Article"Could not capture docker logs" error
Hi, I'm encountering an error I can't explain while testing a new method (MELT; see http://melt.igs.umaryland.edu/) on a single ~30X human whole-genome sample in FireCloud. The error message returned...
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