Estimates of analysis cost with Google Cloud backend?
Are there any estimates of analyses costs with the Google Cloud backend? What happens to zombie/rogue jobs (e.g. max out RAM and hit swap, stalls for whatever reason)?
View Article"Aborted" status in a running job
Hi. When I'm running a batch of samples on FireCloud, some of the jobs finished quickly, however some jobs keep "running" for days. And I check the Monitor, it shows that this job is in an "Aborted"...
View ArticleBest way to pass a parameter into a method
I'm setting up a method that is based on an executable that has multiple functions. When run from the command line, the user chooses the function by passing in a string. For example: bamUtil trimBam -L...
View ArticleHow to remove a method from a workspace?
In the course of development, I needed to modify the wdl for a method. I had already attempted a test in my workspace, but it failed. I redacted the copy stored in the FC Methods Repository. I modified...
View ArticleWhere to find error log for failed analysis?
An analysis performed with a new method failed. The workspace in which it was run is highlighted in red in my list of workspaces. I can browse into that workspace to the Monitor tab and see the list of...
View ArticleMoved: ERROR MESSAGE: Unable to read index file, for input source:
This discussion has been moved.
View ArticleMoved: ERROR MESSAGE: Code exception (see stack trace for error itself)
This discussion has been moved.
View ArticleCan't export/import method broad_cga/contest_mutect_oncotator#2
Hello, We're trying to use method broad_cga/contest_mutect_oncotator#2, but when we attempt to export it into a wordspace nothing happens.. We never see a "Success" message, and the method...
View Article[Bug] Edit a workspace configuration that references a redacted repository...
We have a workspace with a method configuration that references a now-deleted repository method. From the UI, if I click on the method configuration in my workspace, I get an error "Cannot get...
View Article"GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" running...
Some of my samples on Firehose running the task "GATK 4 ACNV Get Bayesian Hets Using Tumor and Normal for Capture" failed due to what seems like memory errors. An example error log is below: Picked up...
View ArticleHow can I change the name of a firecloud project?
I would like to shorten the project name "broad-firecloud-gdac" to "broad-gdac" ... how may I go about this? Thanks, Mike
View Articlejava.lang.OutOfMemoryError in RNAseq workspace
Hi, I have been trying out the new RNAseq pipeline and got an error in one of my samples: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp [Wed Oct 19 22:40:13 GMT 2016]...
View ArticleHow can I delete an entity, and how can I remove an attribute from an entity?
For workspaces, I can delete attributes using this endpoint https://api.firecloud.org/#!/Workspaces/updateAttributes. Is there an endpoint to remove an attribute from an entity? I know it's possible to...
View Article[API] Paginated version of submissions endpoint?
Is there a paginated version of this endpoint (https://api.firecloud.org/#!/Submissions/listSubmissions)? I've already submitted over a thousand jobs in a workspace, it would be nice to be able to...
View ArticleSamtools fails with an error
Hi, I've been trying to run a samtools WDL file on local and it has been with an failed state error. Attached is a screenshot for reference. Can someone please spot the issue and help me run this...
View ArticleAn issue trying to modify workspace attribute values?
Hi, when I try to edit a workspace attribute, the cursor seems to always jump to the end of the field after every character. This makes it rather difficult if I'm trying to add in text at the...
View ArticleMethod to force overwrite when copying entities between workspaces
I was using copy entities endpoint (https://api.firecloud.org/#!/Entities/copyEntities) but encountered a problem during repeated copies. For example, I was trying to copy two sample sets, TCGA-ACC...
View ArticleLock wait timeout exceeded when using the entity import api & UI
Sometimes when trying to import entities, I get a "lock wait timeout exceeded" error and a stack trace. I've gotten this from using FISS and from the UI: firecloud.errors.FireCloudServerError: 500: {...
View ArticleLogin errors/ multiple issues
Hello, several weeks ago I completed the new user registration and created a google billing account following the instructions on the firecloud documentation page. Things appeared to be successful, and...
View ArticleUploading a method with a synopsis longer than characters fails without error
Hey FireCloud team, When creating a new method, devs have the option of adding a synopsis. However, there appears to be a silent character limit to this field. If a synopsis longer than 80-100...
View Article