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ErrorReport(rawls,Unable to query the method repo.,Some(502 Bad...

I got a weird error message submitting my workflow. (1/100 jobs got this message, which is strange.) "ErrorReport(rawls,Unable to query the method repo.,Some(502 Bad...

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Friendly feedback: better error messages

Hi team, @gauthier and I were just looking at some jobs she was running in FireCloud and a bunch of them apparently failed. The error message we see when we click on the "Failures" link states:...

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"Failed to localize files" failure message when running task on sample_set

Hello! I'm trying to run a task (designed for samples) on a sample set by doing: "Define expression: this.samples", but the task failed on all 20 samples in the sample set with the following message:...

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Prerequisite expressions (firehose parity)

Hi Firecloud team, I am trying to use Firecloud, and am moving workflows from FH to FC. I am finding this is impossible because I cannot set pre-requisite expressions. (e.g. do not submit a job if...

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Long submission delay - still

Hi Firecloud team I know there's a post about this, but there's no response. I am also getting long submission delay Is this a current issue? can you confirm that? -Dimitri

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Why can't I set an Expression for an entity?

Lets say I created a new entity annotation under on the participant level called "related_participants" Now I want to run a task on "related_participants" for a participant I would write:...

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Premature connection close (the server doesn't appear to support request...

I enter a workspace and I try to download the sample TSV and instead I get a stack trace (seen below) with the message. Isn't this a known issue? I think I've seen this before... I suspect that the...

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Limit concurrent execution

I want to run a largeish cohort (1000+ individual jobs), but I want to limit concurrent execution to 100. Is there any way to run at most 100 at a time? (this is because they are all making calls to...

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Analysis fails because "no storage left on device"

My mentor has given me a simple WDL method and a dataset to perform a GWAS on. She has already been able to get the method working on firecloud. When I launch the analysis, however, it fails after 15...

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GUI for copying entities is buggy.

I created a new workspace and am copying a single pair into that workspace. The widget for selecting pairs to copy displays columns for participant, case_sample and control_sample. The values for the...

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table of workflow inputs confusing and possibly incorrect

I have a workflow that explicitly declares, at the workflow level, all of its inputs. When I view the tabular presentation of the workflow's inputs from the monitor tab, there are three columns: Task,...

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failing to get size of file

The QC workflow that we run on BAMs before running mutect is failing on a particular data set. The data files in this set reside in a non-workspace, protected bucket that I have read access to...

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what triggers "Unexpected failure in EJEA (root cause not captured)" message?

We have been running WDL workflows that retrieve files (bam and bai in this case) from the GDC. We have been experiencing intermittent failures. When failures do occur, Firecloud reports the following...

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RFE: Launch Analysis... should only list entities a method configuration can...

For method configurations that specify entity attributes as inputs, entities without those attributes should not show up in the "Launch Analysis..." dialog.

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observing delays

this is related to http://gatkforums.broadinstitute.org/firecloud/discussion/9729/long-submission-delay-still#latest and to...

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"Internal Server Error" on entities API calls

I'm getting the error with following calls: https://api.firecloud.org/#!/Entities/getEntities https://api.firecloud.org/#!/Entities/browserDownloadEntitiesTSV when querying samples, but not sample...

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Workflow was marked as Failed, but many tasks continued to run after that

My wdl has a scatter statement that submits 50 parallel tasks. One of these tasks failed because it failed to delocalize its output file, and at that time the whole workflow was marked as Failed. The...

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Completed workflows marked as "Running"; outputs not written to data model

Hundreds of my jobs are currently in this state. Many finished running hours ago. Under "Monitor", the status is marked a successful, and the output from the...

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Large loadfiles do not work

I tried to import a loadfile with 23,000 samples. Instead of the dialog box going away and the window saying Success, the dialog box goes away and it does not say success. There is no indication that...

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re-assign ownership of orphaned methods.

We had a team member leave Broad a few months back, and it turns out that multiple methods that we all now need access to under our shared namespace belonged only to him. For all tasks, workflows, and...

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