Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
"Could not open array genomicsdb_array at workspace" from GenotypeGVCFs in GATK 188.8.131.52
I experience Issues with GenotypeGVCFs and GenomicsDB input in the final GATK4 release using the official Docker image. This does not occur using the 4.beta.6 release. It looks like there has been a bug in an earlier beta release with the same error message which got fixed. Is my issue related to that old bug or just results in the same error message? What can I do to debug the issue?
2018-01-10T12:15:04.154516155Z terminate called after throwing an instance of 'VariantQueryProcessorException' 2018-01-10T12:15:04.154547266Z what(): VariantQueryProcessorException : Could not open array genomicsdb_array at workspace: /keep/d22f668d4f44631d98bc650d582975ca+1399/chr22_db 2018-01-10T12:15:04.154561314Z 2018-01-10T12:15:04.620517615Z Using GATK wrapper script /gatk/build/install/gatk/bin/gatk 2018-01-10T12:15:04.620517615Z Running: 2018-01-10T12:15:04.620517615Z /gatk/build/install/gatk/bin/gatk GenotypeGVCFs -V gendb:///keep/d22f668d4f44631d98bc650d582975ca+1399/chr22_db --output chr22_db.vcf --reference /keep/db91e5f04cbd9018e42708316c28e82d+2160/hg19.fa