"Premature connection close (the server doesn't appear to supp">download "sample" data --> "Premature connection close (the server doesn't...
Attempts to download sample annotations from Workspace broad-firecloud-pcawg/damage result in error message: "Premature connection close (the server doesn't appear to support request pipelining)" This...
View ArticleClicking single Data Entity in Monitor tab on Workflow run on pair set takes...
Hi Firecloud, I ran a workflow on a pair set. The workflow returned succeeded for all but one pair in the pair set. When I go into the Monitor tab, and click on any pair to check the Calls made in the...
View ArticleAll Job Submissions currently stuck in "Submitted" state
Hi Firecloud, It appears that all of my jobs currently get stuck in "Submitted" state, without any update on status (see attached screenshot). When going to the Submission ID google path, it is empty,...
View ArticleGoogle credentials are invalid: connect timed out
Chip submitted a job. Some starting tasks ran okay, but a middle task did not start. I suggested to him to inspect the network tab. Upon inspection, we saw the message here: "failures": [{ "message":...
View ArticleWorkflow is marked as "Running", but the instance seems dead
When submitting my workflow in FireCloud (consisting just of one task), I mistakenly specified only 3G of memory for 4 cores, so all the Java jobs run from inside the Queue script were failing with the...
View ArticleIs firecloud broken?
I'm submitting jobs and they do not run, they remain in "Submitted" mode....these are configurations that have worked in the past...
View ArticleError in "MutationCalling_QC_v1-1_BETA_cfg" method
Hello @birger @mhanna When I try to launch an analysis with "MutationCalling_QC_v1-1_BETA_cfg" in Firecloud, I have an error in the tasks called normalMM_Task and tumorMM_Task. I think that that the...
View ArticleWhen will cromwell 25 be integrated into FireCloud?
On this forum it has been stated several times that problems we are currently encountering with cromwell losing state synchronization with Google Genomics API / JES (e.g., duplicate jobs, jobs that run...
View ArticlePerformance Issues
Hi I have been trying to run the same workflow configuration in the FireCloud and locally. As the FireCloud has been experiencing some issues over the last few days, I've tried to run everything again....
View Articleroot entity type is stuck on participant during method config import?
when I try to take a WDL and import it into my workspace, I try to set the root-entity-type to be pair, but even if I select pair, it goes back to participant. I don't think I saw this before and I've...
View Articleissue related to pushing to method repo. didn't work from workspace, but did...
I have a WDL. I tried to "push" it to the method repo. To do so I went to a workspace, where I would next want to import it to be a config. So I click the "Import Configuration..." button under the...
View ArticleExcessive retries when delocalizing a missing file
My job crashed due to a problem in my code or inputs. It happens. As a result, none of the dozen files the job was supposed to produce were created, so when the delocalizer attempted to copy them back...
View ArticleHow do I track my firecloud spending?
How can I track my current spend in firecloud? When I look in my google billing interface, I don't see any projects related to firecloud and so I am not seeing any way to track my firecloud spend,...
View ArticleSharing methods is difficult, could be better.
Hi Firecloud team, I am trying to share a method I ran in a workspace with another analyst. What I have to do now is 1) Find the exact version of the wdl in the method repo 2) share that exact version....
View ArticleCloning Data Libraries to Workspaces
Hey fire cloud team - Just have a very short question. When I clone a tcga data library (Screen Shots 1-3), it generates a workspace with the name I selected (Screen Shot 4). However, when I tried to...
View Articleworkflows have not worked since yesterday
Hello. I can't to launch any workflows. They are submitted but then they are failed. The messages about errors are empty. It is true for all workflows, even those worked correctly yesterday. Could you...
View ArticleSnapshot ID in listSubmissions API call / Monitor
It would be very helpful if the snapshot ID of a method were included in the output of this call (https://api.firecloud.org/#!/Submissions/listSubmissions) and displayed under the 'Monitor' tab. The...
View ArticleError 500: None.get
I'm trying to clone a workspace and get this error. I wonder if this a known issue? Has anyone else seen this I wonder? Workspace intended to contain NIH protected data Error 500: None.get Occurred:...
View Articlebug and saving incorrect wdl
Hello. I created a method snapshot id:1 Then I added this method into workspace. After this I updated the method and selected snapshot id 2 for this method in my workspace, but I had made a mistake in...
View Article"Failed to upload authentication file" error
Among a run of ~1000 samples, one failed immediately with the error "failures": [{ "causedBy": { "message": "Socket closed" }, "message": "Failed to upload authentication file" }] The same sample ran...
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