Clone workspace - Error: Lock wait timeout exceeded; try restarting transaction
Hello, thank you for great tool. I would like to start using Firecloud with GATK4 pipeline. I got free credits, and I am now trying to start analysis with pre-processing workflow...
View ArticleCan I use Interleaved FASTQ?
I have some HiSeq WGS data that it was made available to us as a BAM files, these are co-ordinate sorted and aligned to some variant of b37 by illumina’s Isaac aligner consequently I’ve reprocessed...
View Articlequestion about flowcell_unmapped_bams_list ?
I want to run 3 samples of WGS. I prepared uBAM files from fastq. However, I can't go further due to absence of flowcell_unmapped_bams_list file. How can I make this from uBAM or fastq?
View ArticleDisappearing WDLs
Over the course of the last week I and others have observed situations that when we want to expand a method configuration in either within a workspace or the method repository, the WDL will not...
View Articlejob waited two days to start...
I submitted a wgs_pip_m2_64core job in workspace rebc-oct16/rebc_template on Jan 24th. Three days later the job actually started according to the monitor tab (attached image). No preemption. Why would...
View Articlemonitor tab indicates I've got 1450 active jobs when there is only one active...
Hi What does the 'Queue status:0 Queued; #### Active' mean at the upper right part of the monitor tab (see attached image) ? Currently there is one job running in...
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Workspace knows it has participant metadata but won't show it
Hello! I have a workspace that contains participant metadata but when it first loads, the metadata is not shown. After clicking the columns button, deselecting all columns, and then selecting...
View ArticleInsufficient permission to perform operation in a workspace that I am owner of
I am one of the owner of aryee-lab/dna-methylation workspace. I imported a method configuration from my own workspace to this workspace and when I try to run this method, I am getting an error saying...
View ArticleMarkDuplicates very slow
I am using the Featured Worskpace for PreProcessingForVariantDiscovery_GATK4 with my data to produce a clean BAM for GATK4 Variant discovery analyses using Best Practices....
View Articlebearer token expiration time
Hi, does anyone know if I can (and if so then where or how) to set the expiration of the bearer token for HTTP requests to FireCloud? It looks like it's about 5 min or so, would be great if I could set...
View ArticleFinished jobs not writing back to Data Model
Hi Firecloud, Many of the tasks I ran in the past few days have finished successfully but are not writing back to the data model. This error has been posted in the past, but it appears to be happening...
View ArticleCan we have an option to disable email notifications?
Hi Firecloud Team, Would it be possible to set a checkbox somewhere to not send notifications when workspaces are shared with me? I don't want to filter all emails from firecloud, but I also don't want...
View ArticleIs there a way to delete a firecloud project if no workspaces have exist...
I created a new FireCloud Billing Project, but realized as soon as I created it that I named it incorrectly. I'd like to delete that billing project and create a new one, or change the name of the one...
View ArticleHow can I add a new service account to a firecloud project?
I'd like to grant WRITE permissions to a service account on a firecloud project where I have owner permissions. I tried to Share.. the project with the service account email address, but it's now...
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Jobs stuck in "Running"
Hi Firecloud, Many of the jobs I have run seem to be stuck in a state of "Running" but when I check the Google bucket output, there is only an exec.sh file, and they have been running for many hours....
View ArticleMSMutTect and MSMutSig
Dear, Where can I get the programs or dock image of MSMutTect and MSMutSig to download? Thanks, Leandro
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Scatter jobs don't run
I'm not sure if this is a scatter problem or just a general FireCloud issue. Some of my jobs in the scatter job fail almost immediately with the following error message: message: Task...
View Article"Namespace does not have a local workflow to run"
I am creating a new method under a namespace which I've successfully used before. However I'm now receiving the following error. "Namespace does not have a local workflow to run" What does this error...
View ArticleMutect2 Oncotator failed to delocalize files
I tried to run Mutect2 with Oncotator in FireCloud and it seems like Cromwell is having trouble copying files, though I don't know what that means. I got the following error message. Task...
View ArticleWorkflow failure with no workflow log to debug
I have a workflow that failed in FC, but contains no workflow log to debug. Can I get help getting either Cromwell server logs or the workflow logs for my workflow? broad-firecloud-dsde/Germline-Module...
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