samtools view slice of cloud storage bam not working
Hi, I am working with WGS data, and since it's so huge (upwards of 300 GB in some cases), when I scatter across many instances I'd like to be able to avoid localizing the entire bam for each scatter....
View ArticleMutation Signature Analyzer
Hi!! I am trying to run the Mutation_Signature_Analyzer on the open breast cancer data from TCGA, cloned the breast TCGA workspace, imported the method and used the default configuration, I used...
View ArticleAuth problems for workspace with external data
I have a workspace (broad-firecloud-dsde-methods/Novaseq-TCGA-blood-normals) where I populated the data model with files from another bucket. (I know this isn't recommended, but I didn't set out...
View ArticleDuplicate samples in a sample set
Hi, I'm having trouble managing my sample sets. if I upload (to FireCloud) a Set membership file twice, I get a sample-set with each of the samplesduplicated. This seems like a bug. Also, it would be...
View Article500 Internal Server Error Backend Error
My workflow fails due to "500 Internal Server Error Backend Error". Do you know what is causing this error? Thanks....
View ArticleAccessing user-pays-access bucket in FireCloud workflow?
Hi - there's a bucket that I need to access in my workflow that involves user-pay access. Is there a way from within firecloud to access these data? Will FireCloud make access requests using my project...
View ArticleError running Mutect2
@bshifaw I have been running Mutect2_gatk4 on the firecloud for tumor-normal samples. I successfully ran the analyses on some of the samples. But for two of my samples, I got an error message saying...
View ArticleFireCloud Error: rnaseq-germline-snps-indels
I was trying to run the method rnaseq-germline-snps-indels, cloned from the workspace help-gatk/rna-seq-germline-snps-indels, on some of my RNAseq samples, and all except one failed at the...
View ArticleGATK analysis using Bam files after BWA alignment
Hello, I need to perform GATK analyis on my Maize chloroplast samplea. I already generated bam files after aligning data from my samples with reference maize chloroplast genome. My objective is to look...
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"socket closed" error
Some of my jobs failed immediately after submission with the following error: opendj-priv.dsde-prod.broadinstitute.org:636; socket closed Resubmitting them worked fine. In the same batch, multiple jobs...
View ArticleUnable to view workflow details
Please see https://portal.firecloud.org/#workspaces/regev-development/ATAC-Seq/monitor/951b4432-def9-4e70-bdf6-b46473d1d7c1/c30a0bb5-2740-4d79-8f3a-f7da761ad8fe
View ArticleCoverage file with Mutect2
I want to run MutSig on the WGS oncotated maf generated by Mutect2. However, I don't have the coverage file required for MutSig. How do I get the coverage file for this?
View ArticleError with rnaseq_bam_star
I am trying to run my RNA-seq bams through "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg" pipeline, but all of my tasks failed with the attached error. Do you know what is the problem and how can I fix...
View ArticleWDL validates and runs fine standalone, but crashes when uploaded to Firecloud
I inherited a large block of WDL 1.0 It validates fine on womtool 32, 33.1, and 34, and I've tested that it runs fine on Cromwell 34. However, when I try to upload it to the method repo, via ether GUI...
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I am running into Errors adding users to my project?
I've added users a few weeks back and it was working. Now I get a "Not Found" error. The user is in my Google setup. Do I need to do something elsewhere?
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Firecloud currently down
Hi, I was first getting Timeout errors and now I am getting this error message on the UI. Will this be fixed soon? Thanks.!
View ArticleDocumentation for Oncotator running in Firecloud
The output from the Firecloud oncotator does not match the output that is documented here: https://portals.broadinstitute.org/oncotator/help/ Could you please direct me to where the documentation for...
View ArticleCromwell - GCP subnetwork error
Hello, I am trying to run our workflow on GCP and got past the VPC network issue by naming the VPC default. However, now cromwell seems to be expecting a specific subnet in our GCP project. I tried to...
View ArticlePAPI error code 5. 10: Failed to delocalize files:
I launched an analysis using GATK Mutect2_pon method to create a panel of normals. This analysis has failed – I got a message regarding the error however I do not know how to fix it. There is a problem...
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Download file from link in data model is failing
An external user has notified us of an error when trying to download a file directly from a link in the data model. This is a "Data Delivery" workspace created by the pipeline ops team and the Data...
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