Notebook terminal is freezing
My terminal window only stays stable for about 5 minutes. If I close and reopen the window works just fine. Notebook seems to be working just fine as well.
View ArticleProblem transitioning to new Google Billing Account after free trial
I followed the steps here. I get this error when I try to run a workflow: Task helloUncompressGZ.UncompressGZ:NA:1 failed. The job was stopped before the command finished. PAPI error code 7. Access Not...
View Articlefirecloud cant access project resources - PAPI error code 7, access not...
Hi - I'm seeing the following error when launching my workflow; message: Workflow failed causedBy: message: Task trinity_fusion_wf.TRINITY_FUSION_UC_TASK:NA:4 failed. The job was stopped before the...
View Articleproblem with permission to access to the google bucket associated with a...
Hello, When I try to access a google bucket associated with a Firecloud workspace, I get the following message: "You need the storage.objects.list permission to list objects in this bucket. Ask a...
View Articleparallel upload of data to google bucket in Firecloud workspace
Hello, We have a large set of .bam/.bai files to transfer to the google bucket associated with a Firecloud workspace. We plan to do the upload of the files in parallel, meaning that several .bam/.bai...
View Articleis recursive docker possible?
Hi, Is it possible to have a workflow run in firecloud as privileged, so it can call docker within the docker (recursively)? There's an externally developed pipeline that I'd want to run, where that...
View ArticleSwitching cluster runtime does not preserve the cluster configuration
I switched runtimes on my notebook cluster because I needed a larger computer. When I did that all of the software installed on the cluster disappeared. Is there anyway to image the cluster and...
View ArticleDoes the notebook cluster showdown if you logout of Terra?
I ran an ML job on the notebook cluster which was running fine but overnight. When I came back in the morning the cluster had shutdown and my job was killed. Is that the right behavior? Thanks, Ilya
View ArticleIs Terra/Firecloud down?
I can't login. Get a gcp error. "502. That’s an error. The server encountered a temporary error and could not complete your request. Please try again in 30 seconds. That’s all we know."
View ArticleClik here to view.
Error uploading samples table to workspace
I get the following when trying to upload a 7mb table to my workspace. Is it too large?
View ArticleHow to change billing account/billing project initially assigned to a workspace?
Hi, Could you please let me know how can I change a billing account/billing project that I initially assigned during generation of a workspace in Firecloud?
View ArticleFailure while processing large unmapped bam file as input to cromwell
Hi Team, We are running five dollar pipeline by running Cromwell(v39) on AWS. Whenever we are running our pipeline on small files(~300MB) process is proceeding fine with further processing. But,...
View ArticleHow to exit in the middle of a linear chain tasks in wdl
Hi, I have a sequential of tasks. If I found the output of task1 has an error message "No space on the disk", I would like to exit the analysis. Don't continue with the following tasks. Is that...
View ArticlePlink prefix and wdl
Hi, I am trying to create a WDL that runs plink and takes as an input a prefix to the bed/bim/fam file I am using Cromwell and docker to run it for example: plink -bfile prefix --recode --out prefix...
View ArticleImplementing GenotyGVCFs and GenomicsDBImport in WDL
This discussion was created from comments split from: Picard/GATK MergeVcfs throws errors.
View ArticleConfirm I am getting the right runtime and runtime options
How do I confirm that I am getting the right runtime and where are the different WDL runtime parameters/options described?
View ArticleCan I add the hash of docker container to my snapshot?
runtime { docker: "imagename":HASH memory: memGB disks: "local-disk 256 HDD" cpu: nCores } This would be useful for forcing versioning of the docker image in the snapshot.
View ArticleDocker pull error
I am getting the following docker pull error when working in a project that is using my google billing account instead of the free billing account. Task genoml.train:NA:1 failed. The job was stopped...
View ArticleClik here to view.
View VMs associated with running jobs in GCP
I am trying to view my jobs in GCP. For the free trial account, I do not have have any active jobs in my job history but I do have a VM running in GCP. It's been running since 4/17. See screenshot For...
View ArticleWorkFlow getting aborted intermittently without any exception
Hi Team, We are facing yet another issue with the large file(68GB) processing wherein workflow is getting aborted all of sudden without any exception on AWS enabled Cromwell. This behaviour is not...
View Article