Why does this family of tasks with array inputs repeatedly fail to cache?
Hi again FC team, I've noticed a somewhat unsavory behavior--always failing to hit the call cache--in a very specific type of task. As best as I have been able to determine, the only features that...
View Article504 errors when trying to load workflow details
Hi FC team, As of this morning, we are encountering 504 errors when trying to load workflow details in the FC portal. Here is an example workflow where we encounter a 504:...
View ArticleWhat are hist.bin files?
I have a PoN file with a "hist.bin" suffix. I cannot find information on what tools this file has been created with, and if it is possible to convert the data back to VCF format, so I could use it with...
View ArticleErrors for MuTect2_pon: CalculateContamination
Hi GATK team, Hope you are doing well! When I used mutect2_pon to generate the PON for my normal samples, an error shows up as follows: Task Mutect2.CalculateContamination:NA:1 failed. Job exit code 1....
View ArticleGATK 4.0 Tool returned: Error?
We are using GATK 4.0 pipeline: FastqToSam /data3/tools/gatk-4.0.6.0/gatk --java-options "-Xmx4g" FastqToSam -FASTQ $1_forward_paired.fq -FASTQ2 $1_reverse_paired.fq -OUTPUT $1.unmapped.bam -PLATFORM...
View ArticleWorkflow imports do not work!
I'm trying to write an import statement in one of my WDL files. The import is: import "https://api.firecloud.org/ga4gh/v1/tools/getzlab:CopyNumberQC/versions/2/plain-WDL/descriptor" as CopyNumberQC...
View ArticleClik here to view.
Workflows are getting stuck at various tasks
Hello, I have experienced many instances of tasks getting stuck while running today. In the first screenshot, I have about 227 out of 387 runs that have been stuck in the aborting phase since 11:40AM...
View ArticleNew to the forum? Ask your question here!
We are facing a high volume of spam that we are working to prevent. Due to this, new users are only able to comment on current question threads, not create new ones. Please post your FireCloud question...
View ArticleVariant discovery gatk4 wdl
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleWorkflow failure dependent on FireCloud Billing Account?
I have two identical workflows (broad-firecloud-ibmwatson/CBB_20181127_CGA_WES_Characterization_TCGAControlledAccess_test and...
View Articlegermline variant calling workflow
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleClik here to view.
Bug report: listing of workflow input display incorrect after first page.
In the monitor tab, when looking at workflow-level inputs and you need to page through the input, after the first page, the Task column shows the label name rather than the task name.
View ArticleJoint discovery wdl
This discussion was created from comments split from: Running joint-discovery-gatk4-local.wdl on hg19.
View ArticleClik here to view.
Failure while creating a FireCloud Billing Project
I was assisting a colleague ( Dr. Othon Iliopoulos,ILIOPOUL@helix.mgh.harvard.edu) of Gaddy's at MGH set up a FireCloud Billing Project, using a Google Billing Account he had previously set up. We...
View ArticleMonitoring information not displayed: 500 returned by submissions API
I have a workflow that has run successfully, but I am unable to view any monitoring information during or after the workflow. When I navigate to:...
View ArticleSample metadata bug
I recently noticed that I can't see all of the metadata under "Data, Samples" in the following workspaces, most importantly the cram paths. broad-genomics-data/WGSPD_Glahn_UK_Psychosis_WGS...
View ArticleQuestion about Running Best Practices locally
Hi GATK Team, I am trying to run th PreProcessing Best Practices on my own computer. What I have done are: a) changed COMMENT1-COMMENT4 in the .inputs.json with the right absolute paths point to the...
View ArticleGetting "invalid_grant" error running method starting around November 27
Hello, I maintain an application that uses firecloud on the backend to run an analysis. However, I got a report recently that the analysis was failing and when I went to look at the workspace in...
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 ArticleQueuedInCromwell status
I have hundreds of tasks with status "QueuedInCromwell". Additionally the workflow says "Done" even though tasks are not yet complete. Thanks.
View Article