task marked as Failed but logs and bucket contents have no hint of why?
I have a WDL task that ran in FireCloud that has 3 files to be de-localized by their listing in the output block. The task is one of 17 tasks in a scatter group. The one I refer to here is #9. The task...
View ArticleDuplicate samples in a sample set
Hi, I'm having trouble managing my sample sets. if I upload (to FireCloud) a Set membership file twice, I get a sample-set with each of the samplesduplicated. This seems like a bug. Also, it would be...
View ArticleAre config namespaces helpful/necessary within workspaces?
Hi Team, Over the last couple of days I've had the recurring thought that it's over-engineering to require config namespaces in workspaces. I can understand how for the Method repository such scoping...
View Articlegoogle says job is done but FC/cromwell don't know it is done?
I have a task that is "Running" (in FireCloud), ..... ClipReadsWF.CreateSequenceGroupingTSVHide Call #1: ID:operations/EMTjxKegKxiRwdyOoJGP8Vwg_eDe0bUCKg9wcm9kdWN0aW9uUXVldWU Status: Running...
View ArticleTiming diagram in workbench is not wide enough
In particular the name of the task is chopped off. this means that I can't tell which shard has what status. thanks! here's an example: http://imgur.com/a/l9Af4
View Articlecromwell down now? issue with my account? cannot run anything at all on FC...
this morning during recent moments. I have not been able to run anything on FC. I've tried different WDLS that previously ran. I've tried multiple FC projects and workspaces. I ran a hello world which...
View ArticleStatus in submission view is different from status of workflow
Hi, I have a submission with 100 workflows (that I launched using a sample_set). When I look at that submission it show all the workflow as "running" however, when I look at any individual workflow is...
View Articledata model not being updated after successful run
Hi, I have run a workflow that has many outputs, via a configuration that links the output to columns in the data model. The workflow ended successfully, but the data doesn't include any of the...
View Articleoptional files not localized? bug?
I have an optional File input ("detailMetrics") in my WDL. (see WDL task opening with inputs including the optional input) task generateMetrics_task { String ID File BAM File BAM_IDX File?...
View ArticleCannot access controlled access workspaces on FireCloud
The linkage between my firecloud account and my eRA commons account had expired overnight. I relinked the accounts this morning at 10:10 am, and got a message: Your link was successful; you will be...
View ArticleMethod repo seems down
I get a basically blank page when I try to access the method repo. Also, I get a 503 error when I try to push a method to the repo using Fissfc.
View Articleworkspace listed in API listing but not in UI? Publish allowed me to see it !...
I have a workspace TCGA_BRCA_ControlledAccess_V1-0_DATA_wgs_10_pairs in project/namespace broad-firecloud-benchmark I'm able to see this in the API listing (see attached PDF) when I visit the swagger...
View ArticleFirecloud down at the moment?
It's 4:24PM EST and I try to log into firecloud and I see spinner "Loading user information..." It has been showing this a few minutes now and others have been able to replicate this issue. I saw on...
View ArticleFireCloud unavailable
When I try to log into FireCloud, I get an "Error loading user information. Please try again" and a Server Unavailable dialog message.
View ArticleAssigning attribute to child sample of a pair
I'm running an algorithm on a pair, and (among other things) it generates an output file for both the case and the control samples. But, when I try to assign the output file to self.case_id. I get an...
View Articleworkflows submitted later start running while workflows submitted earlier...
I have two submissions launched about 6 minutes apart: A more recent one: February 24, 2017, 9:45 AM Submitted esalinas/benchmark_prep_one_m_scatter_wxs_n1_standard_32 10_RAND_BRCA_WGS (pair_set)...
View ArticleDocs are out of date
https://docs.google.com/document/d/1SExJeNoxKGBClPYKtGFfQ0K0bGN2nQeuh_iIkxEt3TY/edit The doc above for putting methods into FireCloud instruct me to download and install the FireCloud CLI, but that's...
View ArticleInternal Server Error? False Alarm?
When viewing a file preview, if the file is zero bytes I see the message : "Internal Server Error". When the same file has data, I see the preview and the error goes away. Is "Internal Server Error" a...
View ArticleURGENT: Job is done but Cromwell thinks it is still running?
I made another submission with a task that is marked as "Running" in the UI: CallingGroup_Workflow.CallSomaticMutations_131_Prepare_TaskHide Call #1:...
View Articletask is done but Cromwell marks it as "Running" prevents entire submission...
I have a task that is the last task in the workflow. Its gcloud alpha genomics describe output is: esalina@gtx590:~/benchmarking$ gcloud alpha genomics operations describe...
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