Hi ! When I use GenomicsDBImport and GenotypeGVCFs , I get the following error, I have no problem with running CombineGVCFs with CombineGVCFs, but  CombineGVCFs is too slow.

a) GATK version used : 4.1.7.0
b) Exact GATK commands used : gatk GenotypeGVCFs -R  path/hg38ncbi.fa -V gendb://mydatabase -O rawvariants.vcf
c) The entire error log if applicable.

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 -jar /home//miniconda3/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar GenotypeGVCFs -R /home//workdir/data_single_cell/sperm/hg38ncbi.fa -V gendb://mydatabase -O rawvariants.vcf
21:14:29.330 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/miniconda3/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 25, 2020 9:14:29 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:14:29.494 INFO GenotypeGVCFs - ------------------------------------------------------------
21:14:29.495 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.7.0
21:14:29.495 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
21:14:29.495 INFO GenotypeGVCFs - Executing as lbjiang@mu01 on Linux v3.10.0-327.el7.x86_64 amd64
21:14:29.495 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01
21:14:29.495 INFO GenotypeGVCFs - Start Date/Time: May 25, 2020 9:14:29 PM CST
21:14:29.495 INFO GenotypeGVCFs - ------------------------------------------------------------
21:14:29.495 INFO GenotypeGVCFs - ------------------------------------------------------------
21:14:29.496 INFO GenotypeGVCFs - HTSJDK Version: 2.21.2
21:14:29.496 INFO GenotypeGVCFs - Picard Version: 2.21.9
21:14:29.496 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:14:29.496 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:14:29.496 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:14:29.496 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:14:29.496 INFO GenotypeGVCFs - Deflater: IntelDeflater
21:14:29.496 INFO GenotypeGVCFs - Inflater: IntelInflater
21:14:29.496 INFO GenotypeGVCFs - GCS max retries/reopens: 20
21:14:29.496 INFO GenotypeGVCFs - Requester pays: disabled
21:14:29.496 INFO GenotypeGVCFs - Initializing engine
[TileDB::StorageManager] Error: Cannot lock consolidation filelock; Cannot lock.
21:14:30.336 INFO GenotypeGVCFs - Shutting down engine
[May 25, 2020 9:14:30 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1199570944
***********************************************************************

A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader

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

and last GATK commands used:

gatk GenomicsDBImport \
-V sample1.g.vcf \
-V sample2.g.vcf \
-V sample3.g.vcf \
--genomicsdb-workspace-path mydatabase \
--intervals chr22

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 -jar /home/miniconda3/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar GenomicsDBImport -V SRR630496.erc.g.vcf -V SRR630498.erc.g.vcf --genomicsdb-workspace-path mydatabase -L chr22
21:21:17.641 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/miniconda3/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 25, 2020 9:21:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:21:17.806 INFO GenomicsDBImport - ------------------------------------------------------------
21:21:17.807 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.7.0
21:21:17.807 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
21:21:17.807 INFO GenomicsDBImport - Executing as lbjiang@mu01 on Linux v3.10.0-327.el7.x86_64 amd64
21:21:17.807 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01
21:21:17.807 INFO GenomicsDBImport - Start Date/Time: May 25, 2020 9:21:17 PM CST
21:21:17.807 INFO GenomicsDBImport - ------------------------------------------------------------
21:21:17.808 INFO GenomicsDBImport - ------------------------------------------------------------
21:21:17.808 INFO GenomicsDBImport - HTSJDK Version: 2.21.2
21:21:17.808 INFO GenomicsDBImport - Picard Version: 2.21.9
21:21:17.808 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:21:17.808 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:21:17.808 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:21:17.808 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:21:17.808 INFO GenomicsDBImport - Deflater: IntelDeflater
21:21:17.808 INFO GenomicsDBImport - Inflater: IntelInflater
21:21:17.808 INFO GenomicsDBImport - GCS max retries/reopens: 20
21:21:17.809 INFO GenomicsDBImport - Requester pays: disabled
21:21:17.809 INFO GenomicsDBImport - Initializing engine
21:21:20.496 INFO IntervalArgumentCollection - Processing 50818468 bp from intervals
21:21:20.498 INFO GenomicsDBImport - Done initializing engine
21:21:20.805 INFO GenomicsDBImport - Vid Map JSON file will be written to /lustre/data_single_cell/sperm1/mydatabase/vidmap.json
21:21:20.805 INFO GenomicsDBImport - Callset Map JSON file will be written to /lustre/data_single_cell/sperm1/mydatabase/callset.json
21:21:20.805 INFO GenomicsDBImport - Complete VCF Header will be written to /lustre/data_single_cell/sperm1/mydatabase/vcfheader.vcf
21:21:20.805 INFO GenomicsDBImport - Importing to array - /lustre/data_single_cell/sperm1/mydatabase/genomicsdb_array
21:21:20.805 INFO ProgressMeter - Starting traversal
21:21:20.805 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
21:21:22.001 INFO GenomicsDBImport - Importing batch 1 with 2 samples
21:22:18.128 INFO ProgressMeter - chr22:1 1.0 1 1.0
21:22:18.128 INFO GenomicsDBImport - Done importing batch 1/1
21:22:18.129 INFO ProgressMeter - chr22:1 1.0 1 1.0
21:22:18.129 INFO ProgressMeter - Traversal complete. Processed 1 total batches in 1.0 minutes.
21:22:18.129 INFO GenomicsDBImport - Import completed!
21:22:18.129 INFO GenomicsDBImport - Shutting down engine
[May 25, 2020 9:22:18 PM CST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 1.01 minutes.
Runtime.totalMemory()=1821900800
Tool returned:
true