I am receiving the following error when trying to run GenomicsDBImport:

Using GATK jar /local/cluster/gatk-4.2.0.0/gatk-package-4.2.0.0-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 -Xmx26g -Xms26g -jar /local/cluster/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar GenomicsDBImport --genomicsdb-workspace-path pre_calibration/cohort_database -L file_paths/interval_list.txt --batch-size 50 --sample-name-map file_paths/map_pre_cal.txt --reader-threads 5

13:13:57.383 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/local/cluster/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

May 07, 2021 1:13:57 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

13:13:57.713 INFO  GenomicsDBImport - ------------------------------------------------------------

13:13:57.714 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.0.0

13:13:57.714 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/

13:13:57.716 INFO  GenomicsDBImport - Executing as johnjare@chrom18.cgrb.oregonstate.local on Linux v3.10.0-957.12.2.el7.x86_64 amd64

13:13:57.716 INFO  GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_71-b15

13:13:57.717 INFO  GenomicsDBImport - Start Date/Time: May 7, 2021 1:13:57 PM PDT

13:13:57.717 INFO  GenomicsDBImport - ------------------------------------------------------------

13:13:57.717 INFO  GenomicsDBImport - ------------------------------------------------------------

13:13:57.718 INFO  GenomicsDBImport - HTSJDK Version: 2.24.0

13:13:57.718 INFO  GenomicsDBImport - Picard Version: 2.25.0

13:13:57.718 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5

13:13:57.718 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2

13:13:57.718 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

13:13:57.718 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

13:13:57.719 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

13:13:57.719 INFO  GenomicsDBImport - Deflater: IntelDeflater

13:13:57.719 INFO  GenomicsDBImport - Inflater: IntelInflater

13:13:57.719 INFO  GenomicsDBImport - GCS max retries/reopens: 20

13:13:57.719 INFO  GenomicsDBImport - Requester pays: disabled

13:13:57.719 INFO  GenomicsDBImport - Initializing engine

13:13:57.865 INFO  GenomicsDBImport - Shutting down engine

[May 7, 2021 1:13:57 PM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=26754416640

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A USER ERROR has occurred: Failed to create reader from file:///variant_calls/pre_calibration/per_isolate/E19.vcf.gz

 

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Per the recommendations in other posts about this issue I have:

1. Double checked that there was a .vcf.gz.tbi index file corresponding to each .vcf.gz file and that both the index file and VCF file were compressed.
2. Ran ValidateVariants on the VCF file (see results below)
3. Recompressed and reindex the VCF file using bgzip and bcftools index -t. 

Here is the output from ValidateVariants:

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 -jar /local/cluster/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar ValidateVariants -R reference/streptococcus_macedonicus_pangenome.fa -V pre_calibration/per_isolate/E19.vcf.gz --validation-type-to-exclude ALL

13:07:57.420 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/local/cluster/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

May 07, 2021 1:07:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

13:07:58.393 INFO  ValidateVariants - ------------------------------------------------------------

13:07:58.394 INFO  ValidateVariants - The Genome Analysis Toolkit (GATK) v4.2.0.0

13:07:58.394 INFO  ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/

13:07:58.395 INFO  ValidateVariants - Executing as johnjare@chrom16.cgrb.oregonstate.local on Linux v3.10.0-1160.15.2.el7.x86_64 amd64

13:07:58.396 INFO  ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_71-b15

13:07:58.396 INFO  ValidateVariants - Start Date/Time: May 7, 2021 1:07:57 PM PDT

13:07:58.396 INFO  ValidateVariants - ------------------------------------------------------------

13:07:58.396 INFO  ValidateVariants - ------------------------------------------------------------

13:07:58.397 INFO  ValidateVariants - HTSJDK Version: 2.24.0

13:07:58.397 INFO  ValidateVariants - Picard Version: 2.25.0

13:07:58.397 INFO  ValidateVariants - Built for Spark Version: 2.4.5

13:07:58.397 INFO  ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2

13:07:58.397 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

13:07:58.397 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

13:07:58.397 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

13:07:58.398 INFO  ValidateVariants - Deflater: IntelDeflater

13:07:58.398 INFO  ValidateVariants - Inflater: IntelInflater

13:07:58.398 INFO  ValidateVariants - GCS max retries/reopens: 20

13:07:58.398 INFO  ValidateVariants - Requester pays: disabled

13:07:58.398 INFO  ValidateVariants - Initializing engine

13:08:05.493 INFO  FeatureManager - Using codec VCFCodec to read file file://pre_calibration/per_isolate/E19.vcf.gz

13:08:06.270 INFO  ValidateVariants - Done initializing engine

13:08:06.270 INFO  ProgressMeter - Starting traversal

13:08:06.271 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

13:08:07.145 INFO  ProgressMeter -       T296_01859:358              0.0                 28595        1969804.8

13:08:07.146 INFO  ProgressMeter - Traversal complete. Processed 28595 total variants in 0.0 minutes.

13:08:07.146 INFO  ValidateVariants - Shutting down engine

[May 7, 2021 1:08:07 PM PDT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.17 minutes.

My interpretation is that my VCF file is fine. Is this correct?

Nothing I tried above has solved the problem and I appear to be having issues with more than just one VCF file (but not all). This is not my first time running this pipeline; however, I used a different reference when mapping my sequences the first time. This issue is new and did not occur during the previous runs.