Does FireCloud always allocate VMs from google's us-central1 region
We want to move some data off of our workspaces' multiregional cloud storage to regional storage in order to reduce our storage costs. In order to be able to continue running analyses on the data...
View ArticleBUG: Groups addUserToGroup API response does not conform to swagger docs.
The swagger documentation indicates that a 404 response indicates a User not found error. However entering an unknown user elicits a 400 response. A 404 response is given when the group does not exist.
View ArticleHow do I do a bulk download of multiple methods?
I am using the firecloud online portal and I need to download all the methods from my search result. Is there a way to do this either from the online portal or from the command line?
View ArticleWDL cannot find parameter file that exists in same google bucket
I'm trying to run a simple WDL that runs "samtools mpileup", where one WDL parameter is the name of an intervals file. From FireCloud I enter the intervals filename as follows "...
View ArticleDone in the VM, but no output on firecloud
Hi FC team, From my stderr file, I learned that my task was finished for a couple hours. But now, the status is stucked by "submitted". my workspace:...
View Articlelimit swap space when running WDL using Terra
I've encountered a case where if a user doesn't specify enough RAM to the STAR aligner and STAR has to use swap space, the task will get stuck running indefinitely. Is there a way to limit swap? Thanks.
View ArticleSamtool 'non-existent file' stops the the...
Hello, I am trying to run a version of the joint-discovery-gatk4-local workflow slightly adjusted to run with a SLURM backend (I am running with gatk 4.0.12.0; the json and wdl files are both based on...
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Issue with CPTAC2 Authorization
According to dbGaP, I'm authorized on TCGA, TARGET, CPTAC2, and CPTAC3: The GDC agrees: But FireCloud does not: I'm going to need to do work in FireCloud with CPTAC2 data soon, so it would be good to...
View Articlestorage.objects.list access error for freecredit project
Hi, I ran a modified method 3-Joint-Discovery from workspace help-gatk/Germline-SNPs-Indels-GATK4-hg38. The GVCF input files failed to import. Because it's a trial account, I couldn't modify the IAM...
View Articlemonitoring_image documentation
I see that Cromwell supports specifying a monitoring docker image (https://cromwell.readthedocs.io/en/stable/wf_options/Google/#google-pipelines-api-workflow-options). I set the monitoring_image to...
View ArticleFirecloud jobs stopping unexpectedly - PAPI error code 10. 14
I have submitted a large computation to FC with ~4000 shards across 4 calls, all tasks allowing a few preemptibles. I noticed a number of shards eventually failing with the following code: message:...
View ArticleTasks queued in Cromwell
I started a workflow on March 29th on ~600 samples that completed for several samples but now all the tasks seem to still be stuck in Cromwell (has been the case with almost no movement since...
View ArticleGoogleCloud Project permissions
Good morning, I am trying to add a lab member to my GoogleCloud Project but do not have appropriate permissions. I was reviewing my GoogleCloud billing project 'stoverlabbilling' and noticed that under...
View ArticleNew feature in FC: workflowFailureMode: "ContinueWhilePossible"
Hi, Is it possible to add "workflowFailureMode": "ContinueWhilePossible" as option when lunching analysis? It's particularly helpful in big computations when some jobs fail randomly PAPI error code 10....
View ArticleGenotypeGVCFs GATK 4.1.0.0 error bcf_update_format: Assertion `nps &&...
Hello! I am trying to run GenotypeGVCFs on a set of 12 pooled-seq (50 fish per pool, using a ploidy of 20 in GATK) whole genome samples. Unfortunately I have had recurrent java memory issues ( I...
View ArticleCannot find output when running docker container with cromwell
Hi there, I currently have a method that I now run with Docker and was hoping to put on Firecloud. The way the docker is currently structured, I run a wrapper script within the container and that...
View Articlejava.lang.Exception: The job was aborted from outside Cromwell
Hi Team, We are enabling Cromwell on AWS and using Cromwell version 39. While testing on five-dollar pipeline, we are facing subjected issue intermittently. There are instances wherein some tasks will...
View Articlemessage: Unable to complete JES Api Request; message: Request payload size...
When running a call to combine multiple files into one using a python script I see the following error: • message: Unable to complete JES Api Request • causedBy: • message: Request payload size exceeds...
View ArticleSubworkflow details cannot be expanded
Hi FC Team, As of last night, a few members of our group have noticed that subworkflow details cannot be expanded for running workflows when clicking the Show button next to each subworkflow on the job...
View ArticleSucessfully completed tasks still marked as running
I have several workflows in my workspaces that are marked as still running even though many of them have successfully completed for several hours now (expanding the individual cases reveals that they...
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