FC latency & bucket access today (July 18 2018)
Hi FC team, We have noticed a dramatic slowdown of FC workspace/method config loading, and intermittent but frequent "bucket unavailable" messages popping up in various places, including blocking us...
View ArticleErrors related to connection issues internet proxy
I have aggregate_bismark_output_grch38 method configuration in aryee-merkin/dna-methylation-pipeline-paper workspace. It uses some bioconductor packages to access annotation information from their...
View ArticleIs queueing broken?
I started a set of preemptible scatter jobs yesterday, but these failed in large numbers with the error "The job was stopped before the command finished. PAPI error code 3. Message: You cannot create...
View ArticleGetting lots of "PAPI error code 10. Message: 14" errors
Many of the jobs I launched last night have failed with "PAPI error code 10. Message: 14" errors. First, can we change this error message to something more helpful? And do we know what this error means...
View ArticleUnable to create a new FireCloud workspace
I've created a new billing account, epilepsy-sc-neale, attached to CO 6910090. I go through the steps to add a new workspace, named Epilepsy_Busch_ClevelandClinic_GSA-MD_QC, and I'm getting an error...
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Slowdown & 15m periodicity when checking call cache
Hi FC Team, In the last ~6 hours, I've noticed some unusual behavior when rerunning workflows almost entirely from cached results. This new behavior is causing these workflows to go from rerunning...
View ArticleError! You do not have access to this file.
Hi Yesterday I updated 55 WGS bams in a bucket. I copied the files from /seq/picard_aggregation and verified that the files are in the bucket using gsutil from my laptop, (also from Broad servers, as...
View ArticleOwnership of Entities in FireCloud
Hi, In transitioning users from Firehose to FireCloud we have been asked about the following: Who owns the data and methods in the FireCloud system? Does the Broad claim any ownership of the data or...
View ArticleSlow Call Cache Checking
I've been noticing very slow call cache checks this afternoon. I submitting about 80 samples to a workflow that should have a fair number of call cache hits and then noticed that a subset of these...
View Articlerequest to whitelist Firecloud workspace for high core/high mem GC
We're assessing the performance of 10x genomics software (CellRanger) to process single cell RNAseq data. Using a 64core 240G VM, it takes 7 hours to run our pipeline (down from 12 hours for 32 core,...
View ArticleNeed to include custom interval list in...
Not sure if this is a GATK question or Firecloud question, but: According to this article, it is recommended that a set of intervals be used with BQSR when working with exomes. However, in the best...
View Articlehow to handle multiple ubam files for a sample, each represent a read group.
Please see if following data model files are properly formated participate file: entity:participant_id disease gender age MORL-X6031_50 Otoscope M 53 sample file: entity:sample_id participant_id...
View Article"rawls" error
Hello, When I try to run a method configuration, the following error message appears: cannot find credentials for RawlsUser(RawlsUserSubjectId(105492220035590692689),RawlsUserEmail(******)) I believe I...
View ArticlePAPI error code 5. Message: 10: Failed to delocalize files: failed to copy...
I keep receiving this error when attempting to run my WDL script. I have run the WDL locally without error using the same docker image. I have permission to the files in the google bucket. I believe it...
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unable to reference a bucket object directly in method config
I have a method config that references a file input through a workspace attribute. I wanted to replace the attribute value with an explicit google bucket URL. I got the following error when I saved the...
View ArticleHow to create sample file for samples with multiple ubams, each represent a...
Hi I have WGS samples, each have multiple ubams and each of them for one read groups. My question is how to create sample file for metadata?
View ArticleBreaking change in Cromwell34 - can the version be chosen?
Today's surprise update to Cromwell34 not only killed all of our existing workflows, but appears to have introduced a breaking change: Expecting memory runtime attribute to be an Integer or String with...
View ArticleGetting the same New Data email
I've gotten 7 emails in the past hour of the same message Dear FireCloud user, Heads up! New data has been added to Cellopedia_CIRM_Eggan_iPSC_WGS. Thanks for using FireCloud!
View ArticleCall caching not working reliably.
I ran a multi-task workflow on a sample pair yesterday. The workflow failed due to the Cromwell 34 upgrade. Several of the tasks in that workflow, however, had succeeded prior to the upgrade-induced...
View ArticleProblem in running five-dollar-genome-analysis-pipeline
The running failed: X6031_50_2_8 Workflow ID:2afe3bf7-9d41-4ae9-b934-11b064bebeef Status: Failed Total Run Cost:n/a Submitted:July 31, 2018, 2:20 PM (1 hour ago) Started:July 31, 2018, 3:39 PM (36...
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