Deleting files not in the metadata
I have the following workspace aryee-merkin/TCGA_WGBS_hg19 which has high storage cost. There were quite a few jobs that either failed or aborted and files generated in those runs are still in the...
View ArticlePAPI error code 10 - and 10% of jobs failed
Hi, About 10% of my 1k jobs failed, and looking at the first couple, they indicate: message: Task ctat_fusion_wf.CTAT_FUSION_TASK_CRAM:NA:1 failed. The job was stopped before the command finished. PAPI...
View ArticleTruncated outputs retained
Hi, In an earlier run from last week, totaling about 1k jobs, about 10% of these were reported to have been successfully completed, but when I look at the result files that were retained as products of...
View ArticleAbort single sample from sample set
I launched a workflow that runs on a single sample across an entire sample set. One of the tasks for one sample seems to be stuck, in that the stderr suggests the tool I'm using reached the end of the...
View Articlecost of .bam/.bai files storage in cloned workspace
Hello, I would like to clone a workspace with some .bam/.bai files in the bucket to proceed with data analysis. I am wondering if the cost of data storage will be still associated just with the primary...
View ArticleWhy does data tab display 'There are no rows to display.' when I have FASTQs...
I uploaded my FASTQ files to the Google bucket associated with my workspace and am able to view them by clicking the bucket link in the FireCloud workspace. However, if I go to the workspace data tab,...
View Articlejava.sql.SQLNonTransientConnectionException after finishing workflow
Hi, I encountered a java.sql.SQLNonTransientConnectionException: connection exception: closed after my workflow was completed. I use GATK 4.0.4.0 and this never happened before. I didn't change...
View ArticleUsing NIO with GATK4 HaplotypeCaller
Is GATK4 HaplotypeCaller NIO compatible? If not, is there another version that is? Thanks!
View ArticleCannot clone a workspace
Hi, I try to clone my workspace so I can import configurations but I get an error Code: 504. Also another error is "Server UnavailableFireCloud service is temporarily unavailable". I would greatly...
View ArticleSome of my jobs are hanging on FireCloud without any progress
Hi FireCloud Team, I have scattered 7 jobs in FireCloud. Three of them finished within one hour. But the other four runs for over 4 hours now. FireCloud claimed these 4 jobs are running but I checked...
View ArticleInsufficient Persmissions
Hello, I'm trying to launch CNV Somatic Panel Workflow. However, when I hit the launch analysis button, I get the error Error: insufficient permissions to perform operation on dipg-2018/Noah_Mimi_DIPG....
View ArticleGetting out-of-memory errors while running the worflow for germline short...
I'm trying to run the wdl posted on the gatk-workflows Github page, under the gatk4-germline-snps-indels repository. The wdl is "haplotypecaller-gvcf-gatk4.wdl" I'm attempting to run this wdl locally...
View Article"cannot import name Timestamp" ggplot pandas
I'm getting the following error in a notebook. ImportErrorTraceback (most recent call last) <ipython-input-6-34dfeaf0e457> in <module>() 2 import pandas as pd 3 from StringIO import...
View ArticlePermissions for grantGoogleRoleToUser
Hello, I'm trying to make modifications to the underlying Google project for a Firecloud billing project. I am the owner of the billing account on Google, and the project on Firecloud, so I figured I...
View ArticleMy FireCloud workflow execution can't access files in my account bucket
I wrote a simple WDL workflow to run Picard's MergeSamFiles on a group of BAM files. The execution repeatedly fails with the same error. The script is attached as merge_script.txt. The logfile...
View ArticleMetric collection task stalls
I have a metric collection task that's part of a workflow that I've run on 372 samples. For 2 of those samples, this particular task seems to stall. The task is supposed to read in a BAM file and...
View ArticleRNA-seq STAR fails for inscrutable reason
Hi! I'm running the public method "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg". Though the first task "rnaseq_pipeline_bam_workflow.samtofastq" succeeded, the second task...
View ArticleCannot process enrollment to FireCloud free trial: Error 56
Hi, I just signed up for a new FireCloud account today and would like try the free trial test gatk workflows for my data. After I click on the 'Start Trial' after the login and accept terms and...
View ArticleUnclear error: PAPI error code 10. Message: 14: VM ggp-14729985031179362160...
When I was running one my workflow in aryee-merkin/dna-methylation-pipeline-paper I got this error message: Task call_bismark_pool.merge_replicates:NA:1 failed. The job was stopped before the command...
View ArticleCan I upload data directly from dbGap?
I have authorization to access whole genome data that is stored in dgGaP that I would like to upload to FireCloud. Can I upload the data directly from dbGaP to FireCloud? Can you please refer me to the...
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