error with files with // in google bucket path
Hi Firecloud, I have some files in a google bucket which I am passing into a task with the following path type: gs://[BUCKET_PATH]//[sub_directory]/mybam.bam When running a task with these inputs,...
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search not working for sample_set in data tab?
I cleared some of the browser data and closed then opened my browser and pointed it to FC. Because of the cleared browsing data, I had to log in to my broadinstitute.org account. I go to the data tab...
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all workflows in a submission done, but submission not marked done and...
I have a workflow c94ac5a8-f333-40dd-8f06-518a1f2a1514 that finished about 49 min ago The workflow is the only one in the submission deed0065-ab63-47ec-9398-b2f30cd32cfa Since the workflow is done and...
View ArticleMoved: Bug: Cromwell removes empty spaces from WDL when creating exec.sh
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View Article[ERROR] make_acnv_pon
Hi, I want to build a ACNV PoN from ~1000 WGS sample. I have ran "make_acnv_pon" for many times. But, all of them are failed due to different Java issues. I have no idea how to change the arguments....
View ArticleFailure to delocalize file - how to specify a directory in FireCloud method...
Hello, I am new to WDL programming and running workflows on FireCloud. I was trying to run a workflow using the BamToUnmappedRGBams method. However, I seem to be having a problem specifying the output...
View ArticleJES error code 10. Message: 14: VM ggp-14197713620027335497 stopped...
Hi Does a failure message that ends with: JES error code 10. Message: 14: VM ggp-14197713620027335497 stopped unexpectedly. mean that the VM on which this particular task was running went down and the...
View ArticleRequest Timed Out (submission on sample_set entity with 8891)
I have a WDL and a method configuration for it. The root entity type of the configuration is a sample_set. I have two submissions from this configuration on a sample_set. The number of samples in the...
View Article[ERROR] token_pon_size_update
I ran “token_pon_size_update” two times to build a PoN using hundreds of TCGA blood samples. But, each of them finally failed because of a file transfer issue. Should I try to run the tasks separately?...
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Please make method config version (snapshot id) visible on Monitor tab when...
Presently, when viewing a submission view the Monitor tab in the UI, the method config version is not displayed (see attached example) . This would be very helpful to have.
View ArticleIn Monitor tab: please change Status column verbagfor "Done, but failed"...
At present when a submission fails it's listed in the Monitor tab as "Done" with a little red box icon that contains an exclamation point. It would be clearer if the text instead said "Failed" ... and...
View Articlemultiple Google accounts
User has a Google account and an institutional account (@med.unc.edu). Only the institutional account has been granted permission to the access to the workspace. The user can access the workspace with...
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failed. JES error code 2. Message: Gaia unavailable
I have a task that failed with an error I've never seen before: Gaia unavailable Inside the operations, I see wm8b1-75c:~ esalinas$ gcloud alpha genomics operations describe...
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Timing off : some values reset
I have a submission and a workflow that started earlier today. The first thing in the WDL is a "scatter" step. Some tasks successfully "hit" in call-caching when the submission was started. The "hits"...
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Successful runs not populating the data table
I thought I would post this as a separate question - I think I am having a similar problem to one which was already posted - the outputs of successful runs are not populating the data table in one of...
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Unable to update method config
When I try to update the optional input aggregate_clusters.mRNAcnmf with the value this.mRNA_protein_coding_CNMF_bestcluster in method config Aggregate_Molecular_Subtype_Clusters in workspace...
View ArticleFeature Request: Downloading sample/participant metadata for a specific...
Hello! Every time I want to download sample or participant metadata from a FireCloud workspace for a specific sample_set, I have to also download the sample_set metadata and filter the entire sample...
View Articleminor GUI bug: filename truncated in dialog window for file download
When I click on a gs:// URL to download a file, a "File Details" dialog box appears. If the path of the file on the bucket is long, the filename is truncated. (See attached screenshot. ) Long filenames...
View ArticleWorkspace bucket is suddenly unavailable to workspace owner
I have a workspace that I created as part of my regression test suite for the Single Cell Portal, and I'm experiencing an issue that I've seen pop up every now and then with a bucket in a workspace -...
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Unexpected failure in EJEA :
I actually got this error message for FOUR workflows seemingly at the same time. At present, I have one open in my browser. Other workflows showed a similar message, but I closed their tabs, then tries...
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