If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

Failed to create reader from file GenomicsDBImport

I have run Halotype caller on some samples to annotate cat genomes and am attempting to run GenomicsDBImport with the following command:

java -jar gatk-package.jar GenomicsDBImport --genomicsdb-workspace-path my_databaseA1 -L A1 -V DS06351.g.vcf

This keeps coming up with this error:

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
05:29:07.393 INFO NativeLibraryLoader - Loading from jar:file:/home/users/cawthamy/gatk-package.jar!/com/intel/gkl/native/
05:29:07.849 INFO GenomicsDBImport - ------------------------------------------------------------
05:29:07.849 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.3.0
05:29:07.849 INFO GenomicsDBImport - For support and documentation go to
05:29:07.849 INFO GenomicsDBImport - Executing as [email protected] on Linux v3.10.0-862.6.3.el7.x86_64 amd64
05:29:07.849 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_171-b10
05:29:07.849 INFO GenomicsDBImport - Start Date/Time: August 1, 2018 5:29:07 AM EDT
05:29:07.849 INFO GenomicsDBImport - ------------------------------------------------------------
05:29:07.849 INFO GenomicsDBImport - ------------------------------------------------------------
05:29:07.850 INFO GenomicsDBImport - HTSJDK Version: 2.14.3
05:29:07.850 INFO GenomicsDBImport - Picard Version: 2.17.2
05:29:07.850 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
05:29:07.850 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
05:29:07.850 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
05:29:07.850 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
05:29:07.850 INFO GenomicsDBImport - Deflater: IntelDeflater
05:29:07.850 INFO GenomicsDBImport - Inflater: IntelInflater
05:29:07.850 INFO GenomicsDBImport - GCS max retries/reopens: 20
05:29:07.850 INFO GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from
05:29:07.850 INFO GenomicsDBImport - Initializing engine
05:29:11.102 INFO GenomicsDBImport - Shutting down engine
[August 1, 2018 5:29:11 AM EDT] done. Elapsed time: 0.06 minutes.

A USER ERROR has occurred: Failed to create reader from file:///home/users/cawthamy/DS06351.g.vcf

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Am I doing something wrong?



Sign In or Register to comment.