Is there a way to see in UI the status of all my active jobs, across workspaces?
I just created a slew of new workspaces and submitted jobs from each space. It would be nice to be able to see the status on all of the submitted jobs, across all spaces, from a single place, instead...
View ArticleHow to get the status of running jobs?
Is there some way to get the status of running jobs? I submitted a workflow yesterday (just 4 tasks) which should probably take 4-6 hours to run at most. They have been running for 19 hours so far. But...
View Articleunable to see submissions that aren't my own?
it seems that FC is preventing me from viewing workflow for submissions that I didn't submit. In the monitor tab, I navigate to a submission then, for a workflow listed under it I click on it to see...
View Articleworkspace/realm sharing request for enhancement
I was shared a workspace that was part of a realm. When the workspace was shared with me, I wasn't part of the realm. At that point, in the "Sharing..." screen my name had "Pending..." by it (see...
View ArticleSuccessful jobs marked as failed
Here's an example: Submission ID: c4d079ab-19c3-4315-b630-58a7966d2449 Workflow ID: 94b7d04c-928c-4662-9736-b3828300a694 Metadata 'failures' JSON: [{'causedBy': [], 'message': 'Not Found'}]
View Articlewrite_lines lacks newline at end of file?
I have a task that uses "write_lines" that I've run in FC. See the WDL below. task wl_task { Array[String] some_data File data_lines=write_lines(some_data) command <<< set -x echo "array data...
View ArticleMetadata from 7K samples
I'm trying to copy the bam index metadata from GenomeStrip_Kathiresan_VIRGO_MESA_TAICHI_Hg19bams for ~7600 samples into another workspace with the same samples (clone of GenomeStrip workspace's...
View Articledata model not updated in context of set-submission with multiple workflows...
Chip has a pair set. He want to run the pair set through two workflows "A" and "B" where B is reads outputs from A via the data entity model. Chip ran first workflow A and all the pairs were...
View ArticleNo access is pair set table in data dialog
This afternoon I loaded a couple of new pair sets into nci-chip-su2c-gmail-com/SU2C-LUNG-data. After loading them with a success message, I'm no longer able to look at the pair set table in the data...
View Articleesalinas/MutationCalling_Filter_v1-0_BETA Snapshot ID: 24 fails in 4 of 97 jobs
In workspace nci-chip-su2c-gmail-com/SU2C-LUNG-data workflow esalinas/MutationCalling_Filter_v1-0_BETA failed in 4 of 97 exome pairs. The error message has something to do with CNA in R: Stderr: Error...
View ArticleJES log: ResumableDownloadException in lots of failed TCGA jobs.
I've been trying to run 50 Strelka jobs on TCGA THCA WGS data in workspace rebc-oct16/rebc_template, I've been running into a brick wall of jobs that are unable to localize the bams with JES log...
View Articlefirecloud account associated with non-gmail email accounts.
Is there a procedure for setting up firecloud access for a collaborator w/o a gmail account? Do they set up a hidden gmail account that transparently communicates with their existing email account?
View ArticleRNA PoN
Hello, We want to create an RNA PoN in Firecloud. We already have the workspace setup. Now we need to identify the RNA normal samples in TCGA data sets which are already in Firecloud and other external...
View ArticleWorkflows: 2744 Queued; 4838 Active; 2744 ahead of yours
I've been watching the status in the upper right and it seems that it's been saying "2744 ahead of yours" for several hours now. But the "4838 Active" part seems to be changing however. is this expected?
View ArticleCryptic failure messages
Hi there, I have a method config that worked swimmingly with a single sample, but is failing like crazy on my ~7k sample set. The top level error message is "Unexpected failure in EJEA." Is that...
View ArticleSuggest adding formal definition of "attribute" to the dictionary
Presently the FireCloud dictionary contains a definition for "Workspace attribute," but does not contain a general definition of attribute (e.g. as it may be applied to other entities). There is...
View ArticleWhy is a "samples" attribute attached to sample_set entities, instead of...
I've noticed that when the RESTful call https://api.firecloud.org/#!/Entities/getEntity is issued on a sample_set entity the payload returned contains an attributes sub-object, one of the members of...
View ArticleImpossible to update from a redacted method to new version
Hi Firecloud Team, I updated a new version of my method, and checked the redact previous version button. This locks me out of editing the old configuration (which I would need to do to set the new...
View ArticleVariable machine disk size
Hi Firecloud Team, I am very confused about variable disk size in firecloud WDLs My use case: workflow inputs - (array of files) required disk size - (total size of all inputs)*4 I found a similar...
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