Hi guys.

I'm running into this same error on both GATK 4.1.6.0 and 4.1.7.0.

Trying to follow the GATK best practice on a set of WES data, with Mutect2 calling somatic short mutations. Following [this guide](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132 , I was trying to build the PON vcf.

This is how I call GATK GenomicsDBImport:

```bash

gatk GenomicsDBImport \
  --reference ~/../robots/anno/b37/human_g1k_v37.fasta \
  --intervals ~/work/icc/_i/good.bed \
  --genomicsdb-workspace-path /share/home/na.su/work/icc/pon_db \
--variant /share/home/na.su/work/icc/_o_pon/112_pon.vcf.gz \
--variant /share/home/na.su/work/icc/_o_pon/114_pon.vcf.gz \
--variant /share/home/na.su/work/icc/_o_pon/116_pon.vcf.gz \
--merge-input-intervals=true \
2> /share/home/na.su/work/icc/log_test_genomicsdb.stderr

```

And the error log:

```

09:24:30.823 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/home/na.su/software/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 29, 2020 9:24:31 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
09:24:31.054 INFO GenomicsDBImport - ------------------------------------------------------------
09:24:31.054 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.7.0
09:24:31.054 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
09:24:31.055 INFO GenomicsDBImport - Executing as na.su@Node107 on Linux v2.6.32-754.el6.x86_64 amd64
09:24:31.055 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
09:24:31.055 INFO GenomicsDBImport - Start Date/Time: April 29, 2020 9:24:30 AM CST
09:24:31.055 INFO GenomicsDBImport - ------------------------------------------------------------
09:24:31.055 INFO GenomicsDBImport - ------------------------------------------------------------
09:24:31.055 INFO GenomicsDBImport - HTSJDK Version: 2.21.2
09:24:31.055 INFO GenomicsDBImport - Picard Version: 2.21.9
09:24:31.055 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:24:31.055 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:24:31.055 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:24:31.056 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:24:31.056 INFO GenomicsDBImport - Deflater: IntelDeflater
09:24:31.056 INFO GenomicsDBImport - Inflater: IntelInflater
09:24:31.056 INFO GenomicsDBImport - GCS max retries/reopens: 20
09:24:31.056 INFO GenomicsDBImport - Requester pays: disabled
09:24:31.056 INFO GenomicsDBImport - Initializing engine
09:24:31.514 INFO FeatureManager - Using codec BEDCodec to read file file:///share/home/na.su/work/icc/_i/good.bed
09:24:32.136 INFO IntervalArgumentCollection - Processing 115051860 bp from intervals
09:24:32.344 INFO GenomicsDBImport - Done initializing engine
09:24:32.369 INFO GenomicsDBImport - Shutting down engine
[April 29, 2020 9:24:32 AM CST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2455764992
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:37)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:897)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:617)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Caused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library
at org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:33)
... 10 more
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at java.lang.System.loadLibrary(System.java:1122)
at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:43)
at org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:30)
... 10 more
Using GATK jar /share/home/na.su/software/gatk-4.1.7.0/gatk-package-4.1.7.0-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 -jar /share/home/na.su/software/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar GenomicsDBImport --reference /share/home/robots/anno/b37/human_g1k_v37.fasta --intervals /share/home/na.su/work/icc/_i/good.bed --genomicsdb-workspace-path /share/home/na.su/work/icc/pon_db --variant /share/home/na.su/work/icc/_o_pon/112_pon.vcf.gz --variant /share/home/na.su/work/icc/_o_pon/114_pon.vcf.gz --variant /share/home/na.su/work/icc/_o_pon/116_pon.vcf.gz --merge-input-intervals=true

```

GATK 4.1.6.0 gave pretty much the same error information (except for the veriong session, of course).

It seems to me that GATK can't find a shared library of java. I been done some Googling but found nothing useful. Can anyone lend me a hand? Hope this thread could do some help.

A confusing newbee