Cromwell use errror
I used cromwell to run WDL with the following command java -Dconfig.file=myCromwell.conf -jar cromwell-34.jar run processing-for-variant-discovery-gatk4.wdl --inputs normal.json but with the following...
View ArticleCan we download gatk-test-data and broad public datasets ? Please help to do.
Can we download gatk-test-data and broad public datasets ? Please help to do.
View ArticleUnlink NIH account from Firecloud
Hi, I'm just wondering how I unlink my NIH account from my Firecloud account. The link expires on Jan 20 but I'm just wondering if I can do it sooner. Thanks!
View ArticleSample consolidated uBAM from public data
In public data I am looking for single consolidated uBAM for below files (full list), gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.4.NA12878.downsampled.query.sorted.unmapped.bam...
View ArticleBaseRecalibrator Step Error
I get below error with workflow step "germline_single_sample_workflow.BaseRecalibrator" java.lang.IllegalArgumentException: Could not build the path...
View ArticleHow can I track usage of free credits, to activity level ?
How can I track usage of free credits, to activity level ?
View ArticleMutect on mm10
Hello, I am trying to run mutect on mouse, and getting the following error ERROR MESSAGE: Unable to parse header with error: Your input file has a malformed header: VCFv4.2 is not a supported version,...
View ArticleGCP billing question
I'm looking at our GCP billing account that only has one project linked to it which we use for FireCloud. I see that, starting on December 19th, we started getting charged about $2/day for persistent...
View ArticlePAPI error code 10. 11
I'm getting the following error. Do you know what might be the cause? Thanks. Task atac_align_peaks.MarkDuplicates:1816:1 failed. The job was stopped before the command finished. PAPI error code 10....
View ArticlePre configured pipeline in firecloud, for calling somatic SNP and indels
Do we have any pre configured pipeline in firecloud, for calling somatic SNP and indels ? Input details - normal BAM and tumour BAM Prefer having uBAM split (if exists) as part of pipeline instead...
View ArticleAccount not inheriting permissions when added to group
Hello, I have a couple groups that I'm using to allow service accounts to access my firecloud workspaces. However, I've noticed that if I add a new member to the group, they don't inherit bucket...
View ArticleArgument list too long
I have a task that tries to merge lots of files from a scatter. I'm getting the error: /cromwell_root/script: line 25: /usr/bin/java: Argument list too long. Is there anything I can do to make this...
View ArticleError: Not enough resources available to fulfill request
I am just starting to use FireCloud for data analysis. We are currently on the free credit program and want to start our first analysis. Our workspace name is: "fccredits-iron-jade-XX31/XXXXX_free“....
View ArticleImporting a workflow that has subworkflows from dockstore to firecloud
If i’m importing a workflow from dockstor to FC is there a proper way to import the subworkflows within the workflow? 1. Should i import using github raw file url. This may be the easist way since i...
View ArticleFailed to parse WDL: ERROR: Finished parsing without consuming all tokens....
Getting the following error when importing a wdl from dockstore to a firecloud workspace. Looks like its having trouble with the line version 1.0, which is the first line of my workflow. Error: Failed...
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Method: broadgdac/mutation_signature_analyzer
Hi! I'd like to try this method (https://portal.firecloud.org/#methods/broadgdac/mutation_signature_analyzer/19) on some of my samples that I analyzed using the best practices Mutect2 workflow. I have...
View ArticleCan't publish docker image to GCR
Hi! I'm trying to publish my own docker container image to GCR (following the instruction Doc#11558) and getting error: denied: Token exchange failed for project [PROJECT-ID]. Caller does not have...
View Articlecannot run "CGA_WES_Characterization_Pipeline_v0.1_Dec2018" pipeline for...
I try to run the "CGA_WES_Characterization_Pipeline_v0.1_Dec2018" pipeline for paired tumor analysis on Firecloud. A common error that I get is “expected single value for workflow input, but evaluated...
View ArticleWhen I create a workspace I do not have access to the google bucket
I created a workspace yesterday afternoon, and got the message: The Google bucket associated with this workspace is currently unavailable. This should be resolved shortly. If this persists for more...
View ArticleNotebooks: using (my own) tools in docker
Hi! I'm trying to move my analysis workflow to R notebook in FireCloud. Is there any way to incorporate my own tools in docker into FC's notebook? Thanks!
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