Is there a standard egress fee?
I would like to know if the egress fee for downloading is standardized. How much would it be to download lets say 10Gb onto my personal computer?
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Setting up the data model for Map variables.
My wdl is expecting a map and the method config reads it as such. How should the data model be set for using maps as input for the method config?
View ArticleData Model Magic
Sorry for repost, was for some reason in "Zoo and Garden!! Hi All, Stuck again. The first step in my pipeline is to convert fastq -> unaligned BAM, which was successful. This is done so that there...
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 ArticleWorkflow and task failures
Hello! I'm running a WDL on several (1200+) genomes and so far, all of them have failed. I'm getting different errors that appear to point to similar, or maybe the same, problem(s). Some examples are:...
View ArticleWorkaround for the GenomicsDBImport + Draft Assemblies + Firecloud = World of...
OK, so my enthusiasm is a bit reserved now that I've gotten to the final phase, joint calling! My naive approach was to hack up the lovely featured WDLs to ignore BQSR, etc. to produce first-round...
View Articleservice accounts, proxy groups ... recently lost access to data
Recently a user (Eric - @ericco92 from NCI) lost ability run jobs in workspace rebc-oct16/rebc_template using data located on the google bucket corresponding to workspace...
View ArticleCross product between entities for Mutect2 normal-normal analysis
What I want to do One of the standard evaluations of somatic variant callers is normal-normal calling, where you take a bunch of replicate normal (non-tumor) bams from the same individual eg NA12878...
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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 ArticleTask hanging without producing JES log/stderr/stdout
Hello, I have a task in Firecloud that will start and will hang without producing a JES log, stderr or stdout file. Even stranger, if I do not cache calls, outputs will be produced in the google...
View ArticleWorkflow failed
Hello, I am submitting jobs in the firecloud with the five-dollar-genome-analysis-pipeline. One of my job failed in the germline_single_sample_workflow.SplitRG step. Here is the error message. message:...
View ArticleAnalysis tab should work on compressed vcfs and allow hg38 reference
The current analysis tab is currently almost unusable. It seems to only allow bam and vcf files, and it only has hg19 reference. The broad's main analysis pipeline is HG38, and produces compressed vcfs...
View Articlegatk/haplotypecaller-gvcf-gatk4 hangs up on Firecloud
Hello, The gatk/haplotypecaller-gvcf-gatk4 workflow on Firecloud starts and hangs without producing a workflow log, JES log, stderr or stdout file. I noticed that in runtime section for each task in...
View ArticleWDL workflow fails in Firecloud due to locating a directory but works in...
I have a WDL workflow that is based on Rscript and it works fine in local cromwell environment when I provide relative paths for the functions. But the same WDL fails in FireCloud. I was able to...
View ArticleWorkflow failures
Some of my samples failed the first time I ran them through an analysis workflow so I restarted them, and now some are still failing with this error: ErrorReport(rawls,http error calling uri...
View Articletask config name mangling in monitor tab
When I launch a task config, its name shows up in the monitor tab. If I later modify the task config (eg update the wdl snapshot or edit the fields), all previously launched task configs now show up...
View ArticleIs there a generic "haplotype map" file publicly available on a FireCloud...
Hello there --- I was wondering whether there's a generic haplotype map file for use with such Picard tools as CheckFingerprint publicly available on a FireCloud workspace (cross-posted here as...
View ArticleError: Lock wait timeout exceeded; try restarting transaction
This evening all FC operations (loading pair_set entities or launching jobs) in workspace rebc-oct16/rebc_template have resulted in a message: Error: Lock wait timeout exceeded; try restarting...
View ArticleRun test on sets with some lacking files
Hi all, I am currently trying to run a method where I basically merge 300 files (.bai files for examples) from all my samples. I get that error message: 2018/03/25 17:14:20 E: command failed:...
View ArticleJobs stuck in 'starting' status
I've been unable to run jobs for the past ~16 hours. For successful submissions, jobs get stuck in 'starting' status. Others in the lab are seeing these problems as well, but status.firecloud.org seems...
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