funcotator error
Hi, FireCloud team Sorry for the duplicated question. I just want to update the format. I ran into a problem recently coming from Funcotator. I initially run Mutect2 coupled with Funcotator on...
View ArticleTabix-incompatible file creation times
I have a workflow that indexes a vcf.gz to produce a tabix index (tbi). A common sanity check when reading from a VCF index is to verify that the index was created more recently than the VCF. It seems...
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The Google bucket associated with this workspace is currently unavailable
2 users have reported in the past 2 days that the Workspace Summary banner shows "The Google bucket associated with this workspace is currently unavailable" error with a link to seek help at...
View ArticleQuestions about billing@firecloud.org's GCP billing role
I have 2 questions about billing@firecloud.org's GCP billing role: (1) This FireCloud article (My billing account isn't showing up or has an error message) says billing@firecloud.org should be a...
View Articleno space left on device error when using latest gatk4 release from gcr
Hi, I'm getting the following error when i try to use the gatk4.0.5.0 gcr image that was released today. (us.gcr.io/broad-gatk/gatk:4.0.5.0) failed to register layer: Error processing tar file(exit...
View ArticleHow to access data in Google Cloud bucket from FireCloud?
I have data already in a google cloud bucket, and I used the same Google cloud account singed into FireCloud. How do I access the data in the google cloud bucket from FireCloud? Thank you.
View ArticleDownloading metadata only from certain rows
Currently when you view the table in the data tab you can view only certain columns and when you download the metadata you only get those columns. This is great! I want to be able to do that for rows...
View ArticleHow to loop all pairs of each participant?
Hi, Say that we have several participants with several pairs. For each participant, we want to merge all VCFs (pair1.vcf, pair2.vcf ...) from each pair into one VCF (participant.vcf). So, what is the...
View ArticledbGAP whitelist for controlling access to CPTAC project data
My understanding is that for TCGA and TARGET studies in dbGAP FireCloud consults a whitelist to determine who is authorized to see the controlled-access data within FireCloud workspaces. A few months...
View Articlejob running(?) for 5 months but status == failed?
Can someone help me interpret what is going on with this job? The cost is at 500$ which makes me think this is still running despite being failed for 5 months......
View Articlegroup name for TCGA Controlled Access Authorization Domain should be changed.
Currently the group name for the TCGA Controlled Access Authorization Domain is dbGapAuthorizedUsers. Once we get support for the TARGET Authorization domain in place, we are probably going to want to...
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Job failing due to "Error getting access token for service account"
I'm running the mutect2-gatk4 workflow on 402 pairs. One of the 402 workflows failed, with reported reason "Error getting access token for service account" (see screen shot below). Based on the log...
View ArticleFeature Request: Collapse display of optional parameters in method config...
A workflow may contain hundreds of input parameters. Quite often the majority of these input parameters are optional and are rarely assigned valued in a method config. It would be very useful if there...
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Billing Alert - 100% of Budget Exceeded
Hi Today I'm getting an email from CloudPlatform-noreply@google.com warning that billing project <not sure billing id's are ok to list on the forum> had reached it's monthly limit of $5K. I've...
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The Google bucket associated with this workspace is currently unavailable
2 users have reported in the past 2 days that the Workspace Summary banner shows "The Google bucket associated with this workspace is currently unavailable" error with a link to seek help at...
View ArticleFire-dollar-genome workflow - "does not have storage.objects.get access to"...
Hi Team, I am trying to run the Five Dollar Genome Workflow on my WGS data which is in a bucket say gs://mybucket/s1.bam. The bucket and bam file is under my google account. The same google account is...
View ArticleFive-dollar-genome workflow failed: HaplotypeCaller4:39:1 exited with return...
Hi, I have been trying to run the five dollar genome workflow on my WGS data, but failed after running for more than 24 hours. The error is from HalotypeCaller4 as below. Any idea what I should? Thank...
View ArticleError running "gatk/PreProcessingForVariantDiscovery_GATK4" on FireCloud
Dear GATK4 team, This is Bo from the Broad Institute. I am running "gatk/PreProcessingForVariantDiscovery_GATK4" on my data in FireCloud and got the following error message: Workflow failed causedBy:...
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Job aborting for a month
Hi, I have a job that has been aborting for a month. I don't know how to handle this bug. I tried to delete the associated bucket, but nothing happened. Any tips? Also, I won't be billed one month of...
View ArticleFireCloud appears hung
I have several workflows in a "Running" state but that are not outputting to stderr or stdout. This is making me thing there must be an issue with FireCloud queuing, and that my jobs are actually hung...
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