Workflow failing due to "Quota CPUS exceeded in region us-central1"
Several of my workflows have failed recently with "quota exceeded" errors. See for example the workflow with id 1c243834-ca4c-4e3e-a940-2ae3c1f9f57e that fails with this message: message: Task...
View ArticleSearch bug?
So I've got a workspace with 1000 participants whose IDs are numbers: https://portal.firecloud.org/#workspaces/broad-firecloud-dsde-methods/gnomad_scale_testing/data (I've shared this workspace with...
View ArticlePublic method configurations are no longer visible/accessible
For example, this method should have two public configurations: https://portal.firecloud.org/#methods/broadinstitute_gtex/star_v1-0_BETA/2 But the 'Configurations' tab shows "You don't have access to...
View ArticleBUG: Unable to set optional Int fields in method configs
If I reopen, or look at the inputs of a launched method config in which I have set an optional Int field to any integer value, I see in the reopened config that it remains unset, and in the monitor...
View Articlebehavior of workspace attributes downloading
I have a workspace broad-firecloud-eddie/eddie_test_contam_Broad_MutationCalling_QC_Workflow_BestPractice_copy_copy_explore_wsattr I download the workspace attributes (by clicking "Download...
View ArticleIssue with creating workspaces via the API
I'm seeing issues with creating workspaces via the API for the Single Cell Portal. When I POST to api.firecloud.org/api/workspaces with a workspace payload object, on occasion my application will throw...
View ArticleErrorReport(rawls,Unable to query the method repo.,Some(502 Bad...
I got a weird error message submitting my workflow. (1/100 jobs got this message, which is strange.) "ErrorReport(rawls,Unable to query the method repo.,Some(502 Bad...
View ArticleDoes "Save As New Snapshot" still work in the Edit Method pop-up dialog?
Hi I've been attempting to update a workflow in FC stewart/SamtoFastq (simple picard conversion from bam to fastq files) but the "Save As New Snapshot" doesn't appear to do anything. As a clueless FC...
View Articlefailed on the pipeline of BamToUnmappedRGBams_MC
I jut got this error: message: Job BamToUnmappedRGBamsWf.ValidateSamFile:0:1 exited with return code 3 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute...
View ArticleMoved: failed on the pipeline of BamToUnmappedRGBams_MC
This discussion has been moved.
View Article[ERROR] the local copy message must have path set.
Hi Firecloud Team, I submitted a workflow to FC yesterday. But, just one of the tasks was failed. I tried three times and got the same ERROR message as following in workflow.log. And, there is no log...
View Article[OUTPUT] Invalid output expression: this.WXS_Mutation_M1
Hi Firecloud team, The workflow has been done. But, the output data is not able to add into the entity attributes. Previously, this WDL always worked well on FC, but no this time. Please help me to...
View ArticleCan I define a temporary output file that is not retained at the end of a...
I have a workflow that creates a number of large intermediate files that are passed between tasks. These files do not need to be retained at the end of the workflow (and take up a considerable amount...
View ArticleAccessing firecloud workspace API with service acccount
I have made a service account through a non FC project. I saved the json file for this account with me. The following piece of code is written so that Firecloud api is accessed with service account...
View ArticleBUG: Array[File] populated by read_lines() does not get delocalized paths
I have a script that writes out the relative paths (i.e. ./path/to/file) of its varying outputs to a file. in the output block of my WDL, I populate an Array[File] with these path via read_lines()...
View ArticleSmall feature request - name downloads of metadata by workspace
Right now my downloads directory looks like this: $ls -1 ~/Downloads/participant*.txt /Users/dlivitz/Downloads/participant (1).txt /Users/dlivitz/Downloads/participant (2).txt...
View ArticleProblem installing fiss for firecloud
Hi, I'm trying to install fiss for firecloud on my local computer, and I'm getting the following error (downloaded the source from github repo): WMBB1-789:fiss-master chrislo$ sudo python setup.py...
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not taking advantage of pre-emptibles during holiday?
i logged in to FC during the morning to kick off some jobs expected to take a day or so to run. My idea is to use pre-emptibles over the thanksgiving holiday based on the presumption that there might...
View ArticleSpecifying a file in a google bucket as a string input to a task in a wdl
Hi Due to how data fields in a vcf were labeled I need to parse bam names in a vcf_parsing task, but I don't actually need (or want) the bams to be localized. I had expected that an input block like...
View ArticleGATK on Google Genomics scale up quota recommendations
We managed to analyze our own full genome data following the recommondations on GATK on Google Genomics. When we launch the analysis for a single sample, output is produced within 24 hours, with the...
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