We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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 libgkl_compression.so from jar:file:/home/users/cawthamy/gatk-package.jar!/com/intel/gkl/native/libgkl_compression.so
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 https://software.broadinstitute.org/gatk/
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 https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
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] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1194852352


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?

Tagged:

Answers

Sign In or Register to comment.