Hello, I am using Terra to run GenotypeGVCFs on a GenomicsDB that exists in Google Cloud and therefore is a `gs://` URI. I generated it by using `GenomicsDBImport` with the output specified as `gs://BUCKET_URL/genomics_db/chr22` as per the specification stating that users can update a genomicsDB in-place as a GCP URI. I have successfully managed to create the genomicsDB, and am now wondering how to use it as an input for GenotypeGVCFs. Thanks!

a) GATK version used: 4.1.9.0
b) Exact command used:

GATK --java-options -Xmx8G GenotypeGVCFs -R /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta -O chr22.10000001_11000001.margined.genotyped.vcf -L chr22:10000001-11000001 -V gendb:///gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/genomics_db/chr22

c) Entire error log:

2021/03/19 18:56:28 Starting container setup.
2021/03/19 18:56:30 Done container setup.
2021/03/19 18:56:31 Starting localization.
2021/03/19 18:56:37 Localization script execution started...
2021/03/19 18:56:37 Localizing input gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta.fai -> /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta.fai
2021/03/19 18:56:38 Localizing input gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.dict -> /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.dict
2021/03/19 18:56:38 Localizing input gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta -> /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta
Copying gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.dict...
/ [0/2 files][    0.0 B/  3.0 GiB]   0% Done                                    
Copying gs://fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta...
/ [0/2 files][    0.0 B/  3.0 GiB]   0% Done                                    
/ [1/2 files][  5.0 KiB/  3.0 GiB]   0% Done                                    
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- [1/2 files][353.7 MiB/  3.0 GiB]  11% Done                                    
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| [1/2 files][848.2 MiB/  3.0 GiB]  28% Done                                    
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- [1/2 files][  1.3 GiB/  3.0 GiB]  44% Done                                    
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\ [1/2 files][  1.8 GiB/  3.0 GiB]  60% Done                                    
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/ [1/2 files][  2.2 GiB/  3.0 GiB]  74% Done                                    
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\ [1/2 files][  2.6 GiB/  3.0 GiB]  87% Done                                    
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| [1/2 files][  2.9 GiB/  3.0 GiB]  98% Done                                    
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/ [2/2 files][  3.0 GiB/  3.0 GiB] 100% Done                                    
Operation completed over 2 objects/3.0 GiB.                                      
2021/03/19 18:56:46 Localizing input gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/script -> /cromwell_root/script
2021/03/19 18:56:48 Localization script execution complete.
2021/03/19 18:58:08 Done localization.
2021/03/19 18:58:09 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash szarate/t2t_variants@sha256:96fe8147b4a946ae5b687c4c32b2004da1ded105091fab8fb5f6eac0f5ac89dd /cromwell_root/script
Using GATK jar /gatk-4.1.9.0/gatk-package-4.1.9.0-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 -Xmx8G -jar /gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar GenotypeGVCFs -R /cromwell_root/fc-47de7dae-e8e6-429c-b760-b4ba49136eee/t2t-chm13.20200921.withGRCh38chrY.chrEBV.chrYKI270740v1r.fasta -O chr22.10000001_11000001.margined.genotyped.vcf -L chr22:10000001-11000001 -V gendb:///gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/genomics_db/chr22
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.ae432eaf
18:58:12.985 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
18:58:13.148 INFO  GenotypeGVCFs - ------------------------------------------------------------
18:58:13.148 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.9.0
18:58:13.148 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
18:58:13.148 INFO  GenotypeGVCFs - Executing as root@24a30c1028db on Linux v5.4.89+ amd64
18:58:13.148 INFO  GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
18:58:13.149 INFO  GenotypeGVCFs - Start Date/Time: March 19, 2021 6:58:12 PM GMT
18:58:13.149 INFO  GenotypeGVCFs - ------------------------------------------------------------
18:58:13.149 INFO  GenotypeGVCFs - ------------------------------------------------------------
18:58:13.149 INFO  GenotypeGVCFs - HTSJDK Version: 2.23.0
18:58:13.149 INFO  GenotypeGVCFs - Picard Version: 2.23.3
18:58:13.149 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:58:13.149 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:58:13.149 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:58:13.149 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:58:13.149 INFO  GenotypeGVCFs - Deflater: IntelDeflater
18:58:13.150 INFO  GenotypeGVCFs - Inflater: IntelInflater
18:58:13.150 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
18:58:13.150 INFO  GenotypeGVCFs - Requester pays: disabled
18:58:13.150 INFO  GenotypeGVCFs - Initializing engine
18:58:13.516 INFO  GenotypeGVCFs - Shutting down engine
[March 19, 2021 6:58:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=438304768
java.nio.file.ProviderNotFoundException: Provider "gendb" not found
	at java.nio.file.FileSystems.newFileSystem(FileSystems.java:341)
	at org.broadinstitute.hellbender.engine.GATKPath.toPath(GATKPath.java:57)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.getCodecForFeatureInput(FeatureDataSource.java:352)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:334)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:282)
	at org.broadinstitute.hellbender.engine.VariantLocusWalker.initializeDrivingVariants(VariantLocusWalker.java:76)
	at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:67)
	at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:709)
	at org.broadinstitute.hellbender.engine.VariantLocusWalker.onStartup(VariantLocusWalker.java:63)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
2021/03/19 18:58:14 Starting delocalization.
2021/03/19 18:58:15 Delocalization script execution started...
2021/03/19 18:58:15 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/memory_retry_rc
2021/03/19 18:58:15 Delocalizing output /cromwell_root/rc -> gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/rc
2021/03/19 18:58:16 Delocalizing output /cromwell_root/stdout -> gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/stdout
2021/03/19 18:58:18 Delocalizing output /cromwell_root/stderr -> gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/stderr
2021/03/19 18:58:19 Delocalizing output /cromwell_root/chr22.10000001_11000001.margined.genotyped.vcf -> gs://fc-1f86e464-457c-4114-a07d-268cb41f9efe/d677897d-9e4b-49f4-a7bf-13d0eeb1aa9d/t2t_interval_calling/5059d6fe-a94b-4523-8844-aae424726e0a/call-genotypeInterval/chr22.10000001_11000001.margined.genotyped.vcf
Required file output '/cromwell_root/chr22.10000001_11000001.margined.genotyped.vcf' does not exist.