spatel-gfb

Results 6 comments of spatel-gfb

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

Thanks @droazen and @nalinigans , I will try it out and get back with results.

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

Hello @droazen and @nalinigans , we tried out the parameter you suggested and did improve the performance but not as great as compared to writing the data locally and then...

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

Thanks @nalinigans , will it also help in Importing VCFs to the genomics db ?

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

Hello @nalinigans, As part of gatk-sv pipeline we are using GATK : v4.1.8.1 which doesn't have bypass-feature-reader option. Also, we didn’t capture strace for the run with just "--genomicsdb-shared-posixfs-optimizations" so...

SV Pipeline Jobs LongRunning : BAFFromGVCFs_ImportGVCFs and GenotypeVCFs

Thanks @ldgauthier , we will try that option out in few weeks. For now as a work-around for this, we are writing it to local EBS volumes which gives best...

Job Long Running -- Module : GatherBatchEvidence Job : BAFFromGVCFs_ImportGVCFs

More details on further troubleshooting. We are running this pipeline on AWS infrastructure. While running this job on the EBS volumes, the performance seems to be ok, but when we...