TCGA access: eRA sign in requires parsing token
Hi FireCloud team, I used to be able to use my NIH-EXT login credentials to get TCGA access on the iTrust page at auth.nih.gov. Somehow now I'm stuck on the same page when I log in. Not sure why but it...
View ArticleBulky stderr causes node to hang
I was trying to run SamToFastq, using a docker which I have successfully run in the past, via a standalone instance of Cromwell with a JES backend. I believe it is Cromwell version 31, though the...
View ArticleUnable to create a cluster for jupyter notebooks
I've been trying to create a cluster from within a workspace that I have writer access to. I also have permissions to use the billing account for that workspace. However, I keep getting this error:...
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Random errors
I ran a workflow of 100 jobs and 7 just didn't start. I will re-start them but this is a new issue because I used to be able to run 1000+ jobs without issue.
View ArticleBug: help-gatk/Somatic-SNVs-Indels-GATK4/method-configs/gatk/mutect2-gatk4
workspace.ref_fasta_index should be workspace.ref_fai extra space in this. bamout_index
View ArticleHow do I cite tools such as firecloud, WDL and cromwell?
I am wondering whether there are any citations available for tools like firecloud, WDL and cromwell
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Error 400 : Logging into FireCloud with my Google Account
I am getting the attached error on logging into FireCloud with my Google Account. I saw a previous post from someone with the same error (July 2017) that said they thought this was fixed. Still...
View ArticleNovice to FireCloud & BioInformatics
Hi Guys, Im new to the world of sequencing and have started using the Oxford nanopore Tech MinION in my lab. I have managed to do RNAseq and WGS using it and got as far as using terminal to get Bam/Sam...
View Articlescopes required for https://api.firecloud.org/api/workspaces
Hi Firecloud Team, I run a small webapp built on top of the firecloud api for my group. As of very recently started getting: ``Bearer error="insufficient_scope", error_description="Different scope(s)...
View ArticleGoogle bucket path String no longer properly coerced to File in output
Because optional outputs have yet to be added to the WDL spec (an outstanding issue for over two years), we've had to implement a work-around using a generic "null" file: task variable_outputs { File?...
View ArticleFirecloud job seems to be running in loop; neither fails nor completes
I have been using some of the WDL scripts that I wrote with the data in aryee-merkin/colon-seqcapepi workspace. The scripts seems to be working for all the samples that I have tried out so far. For one...
View ArticlePossibly misleading failure message?
I (re-)ran our CGA somatic variant calling pipeline on 402 TCGA THCA pairs. In addition to the expected failures due to congestion in rawls (see...
View ArticleDuplicates in sample sets and participant sets
If you upload a participant set or sample set that has entities that already exist in the workspace, you end up with duplicates in the set. This makes it difficult to add additional entities to a set...
View ArticleMissing file from Firecloud data model -- requesting access to bucket logs
Hi, Ive had a file go missing from my workspace and need access to the gcp logs for my workspace so that I can check what happened. The bucket id is : storage-logs-broad-firecloud-wuclonal Thanks Amaro
View ArticleMutect2 error
I tried to run the Mutect2 analysis, and this error happened: Task Mutect2.CalculateContamination:NA:1 failed. Job exit code 1. Check...
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Job submission hanging for an hour
I have a job submission hanging for an hour is there a problem with dispatch currently?
View ArticleJobs stuck in queued status
Hello, Since around midnight last night to this morning, all of the jobs I have launched are stuck in the "queued" state. This extends from jobs that are run on a single sample to jobs run on sample...
View ArticleProblem running gdc-client tool
I've been trying to run the gdc-client tool to download a bam file into my workspace. The docker image I'm using is docker.io/broadinstitute/gdc_downloader:1.0 The tool itself was downloaded from the...
View ArticleRunning out of memory pulling docker image?
I am having issues pulling a docker image which I know is only 3Gb on to a machine with 50gb (it fails even at 500gb) with the following error: 9da20178641f: Pull complete 5446f6f497ad: Pull complete...
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Where can I find when Firecloud has a scheduled maintenance planned?
So my UI says that there is planned maintenance going on? Is there a place I can see a list of times where I should expect Firecloud to be down? This was around 10:30 AM, 5-17-2018
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