Hi, I'm having a problem with GenomicsDBImport that I have no idea how to solve. The error in question is: A USER ERROR has occurred: Failed to create reader from file:///mnt/fastdata/mbp15jdp/GTEx/SRA-private/SCAPT_gVCF/Variantcalls.dir/Frontal_Cortex-5074-NPJ8.g.vcf.gz
And the following is the statment I am running:
gatk --java-options -Xmx10G GenomicsDBImport -V Variantcalls.dir/Frontal_Cortex-5074-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4565-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4996-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4005-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4435-NPJ8.g.vcf.gz -V Variantcalls.dir/Cerebellar_Hemisphere-4643-NPJ8.g.vcf.gz -V Variantcalls.dir/Cerebellar_Hemisphere-4839-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4434-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4913-NPJ8.g.vcf.gz -V Variantcalls.dir/Cerebellar_Hemisphere-4274-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-5025-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-4262-NPJ8.g.vcf.gz -V Variantcalls.dir/Frontal_Cortex-5037-NPJ8.g.vcf.gz -V --genomicsdb-workspace-path VCFdatabase.dir --intervals chr19
Any help would be much appreciated.
Which version of gatk are you using? Are you running this on the firecloud/NFS system? Also Would you please post the entire error log?
Here are a couple of things you can do.
1) As mentioned in the error log run --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' and send us the stack trace to debug this issue.
2) Try to run SelectVariants with the input vcf to see if this issue is with the vcf or genomicsdbimport.
Please send us your findings once you have done this.
As we have not heard back from you in more than 2 business days, we are closing this issue for now. Please get back to us if you have more questions.