Rerun workflows in failed or aborted state
This is a feature request. Consider the following usage scenario: I launch an analysis on a collection of 1000 samples. 900 of them succeed, but 100 of them get stuck. I abort the submission, but want...
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Unable to view billing information
Hello, I've been using FireCloud for the past two months, and I've recently noticed that I'm no longer able to view the billing information for my free FireCloud credits account. Starting from my...
View ArticleStdout/stderr output in bucket does not seem to be updated while task is running
I have a method/task which I've ran before, during (failed), and after the recent update. For some reason I no longer see anything in the associated bucket folder stdout and stderr log files (these...
View ArticleTransfer of ownership of usergroup for method creation in group namespace
Hi FC team, We have a method namespace called Talkowski-SV on FireCloud, in which members of the Talkowski-Lab-SV group can create methods. The sole owner of that user group left the lab several months...
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Workflows are getting stuck at various tasks
Hello, I have experienced many instances of tasks getting stuck while running today. In the first screenshot, I have about 227 out of 387 runs that have been stuck in the aborting phase since 11:40AM...
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How can I write to the sample level using a pair level method?
I heard this was working before using: this.sample.attribute but I seem to be getting an error saying : "Failed at line 1, identifier part expected." Is this maybe due to the recent update? Thanks!
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Jobs stuck in submitted state or failing without message
Over the last few days, whenever I ran jobs on multiple samples, a small fraction (~5%) either failed immediately without a message (see screenshot) or remained stuck in 'submitted' state for hours....
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Method configurations are not loading (Server Unavailable error)
Hello Firecloud Team, I started to see the same error for the past few days when trying to access method configurations in the method repository. It takes awhile to load configurations but then this...
View ArticleQueued in Cromwell
The workflow I'm currently running seems sluggish this morning. Some tasks say Queued in Cromwell and some jobs are taking 20 minutes to realize its a call-cache hit. I'm wondering if others are...
View ArticleGoogle Cloud Project for Bucket
I'm trying to upload a file to the Google bucket for a FireCloud project using the Java API (https://cloud.google.com/storage/docs/reference/libraries and click on "Java"). I'm open to using other Java...
View ArticleIntermittent problems causing large numbers of workflow failures
Yesterday morning I launched the CGA Production WES workflow on two TCGA cohorts: THCA with 402 tumor/normal pairs and LUAD with 267 tumor/normal pairs. In each case, I got a large number of workflow...
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Transient error providing no error message or log files
Hello, I was running a task on a sample that failed within minutes that lacks an error message or log files (attached). The first time this happened to me I ran the task again without an issue....
View ArticleCharges for failed runs
Hi, As we all are aware there have been some upgrade issues, patches, and fixes on FC over the past weeks. I had several runs (of sets) that failed (several times over) and generated a whole bunch of...
View ArticleAccessing the samples of a participant
It currently isn't possible to access a participant's sample attributes directly, using this.samples.<attribute> This is a significant limitation for analyses across samples (e.g., tissues, cell...
View ArticleAccessing bucket from Notebooks in R
Hello! I'm new to Firecloud and would like to use the Notebooks feature to run some basic data analysis in R on data I've uploaded to a bucket. I see the example notebooks using the Python FireCloud...
View ArticleThe job was aborted from outside Cromwell: How to get around this error?
I am processing a few very large TCGA samples and I am getting the following error The job was aborted from outside Cromwell. My workflows are in aryee-merkin/TCGA_WGBS_hg19 and submission id is...
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How do I make a workspace public?
I see the "Publicly Readable?" check box in my method after clicking the share icon, but i don't see the check box for a workspace I created. How do i make my workspace public?
View ArticleOverwrite returned data in the "data" table upon re-run
Sometimes when we run a workflow, it will complete and return output, but that output will be incorrect. In these cases we may have to, for example, make changes to input parameters or reference files....
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Downloading and Uploading configurations adds quotations
I downloaded the configurations from one method and uploaded to another method. When i did so some of the variables had quotations. Original method config: New method: I recieved the following error...
View ArticleJust signed up but received the message below
The Google bucket associated with this workspace does not exist. Please write our help forum for assistance.
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