Hello

Please find the code used for exporting GVCF to genomic database and the error as well. I tried renaming the interval list file but still get the error. Please advice

Version: GATK/4.2.2.0-foss-2018b-Java-1.8

gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/1.g.vcf.gz \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/3.g.vcf.gz \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/5.g.vcf.gz \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/7.g.vcf.gz \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/9.g.vcf.gz \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/11.g.vcf.gz \
--genomicsdb-workspace-path my_database \
-L /scicore/home/cichon/GROUP/memory_optimization/data/interval.list

Error:

10:54:36.805 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/scicore/soft/apps/GATK/4.2.2.0-foss-2018b-Java-1.8/gatk-package-4.2.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 09, 2021 10:54:37 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:54:37.130 INFO GenomicsDBImport - ------------------------------------------------------------
10:54:37.130 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.2.0
10:54:37.131 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
10:54:37.131 INFO GenomicsDBImport - Executing as thirun0000@shi18.cluster.bc2.ch on Linux v3.10.0-1062.18.1.el7.x86_64 amd64
10:54:37.131 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-b03
10:54:37.131 INFO GenomicsDBImport - Start Date/Time: November 9, 2021 10:54:36 AM CET
10:54:37.132 INFO GenomicsDBImport - ------------------------------------------------------------
10:54:37.132 INFO GenomicsDBImport - ------------------------------------------------------------
10:54:37.132 INFO GenomicsDBImport - HTSJDK Version: 2.24.1
10:54:37.132 INFO GenomicsDBImport - Picard Version: 2.25.4
10:54:37.132 INFO GenomicsDBImport - Built for Spark Version: 2.4.5
10:54:37.132 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:54:37.132 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:54:37.132 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:54:37.133 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:54:37.133 INFO GenomicsDBImport - Deflater: IntelDeflater
10:54:37.133 INFO GenomicsDBImport - Inflater: IntelInflater
10:54:37.133 INFO GenomicsDBImport - GCS max retries/reopens: 20
10:54:37.133 INFO GenomicsDBImport - Requester pays: disabled
10:54:37.133 INFO GenomicsDBImport - Initializing engine
10:54:40.135 INFO GenomicsDBImport - Shutting down engine
[November 9, 2021 10:54:40 AM CET] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=4151836672
***********************************************************************

A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "@HD VN:1.5 SO:coordinate" is not valid for this input.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /scicore/soft/apps/GATK/4.2.2.0-foss-2018b-Java-1.8/gatk-package-4.2.2.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -Xms4g -jar /scicore/soft/apps/GATK/4.2.2.0-foss-2018b-Java-1.8/gatk-package-4.2.2.0-local.jar GenomicsDBImport -V /scicore/home/cichon/GROUP/memory_optimization/variants/1.g.vcf.gz -V /scicore/home/cichon/GROUP/memory_optimization/variants/3.g.vcf.gz -V /scicore/home/cichon/GROUP/memory_optimization/variants/5.g.vcf.gz -V /scicore/home/cichon/GROUP/memory_optimization/variants/7.g.vcf.gz -V /scicore/home/cichon/GROUP/memory_optimization/variants/9.g.vcf.gz -V /scicore/home/cichon/GROUP/memory_optimization/variants/11.g.vcf.gz --genomicsdb-workspace-path my_database -L /scicore/home/cichon/GROUP/memory_optimization/data/interval.list