Hi,

GATK4.2.2.0. is being used.

I am trying to follow the book genomics in the cloud. Create variants GVCF file for mom, father and son. First combine mom and father's GVCF files and select variants from both.

The codes are as following：

java -jar $gatk GenomicsDBImport \
-V ./germline_analysis/father_variants.200k.g.vcf.gz \
-V ./germline_analysis/mother_variants.200k.g.vcf.gz \
--genomicsdb-workspace-path ./germline_analysis/trio-gdb \
--intervals 20:10,000,000-10,200,000

This step is working.

java -jar $gatk SelectVariants \
-R ./data/germline/ref/ref.fasta \
-V ~/GATK/germline_analysis/trio-gdb \
-O ./germline_analysis/duo_selectvariants.g.vcf.gz

after I run this, the information shows:

21:49:03.160 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/jingchun/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 13, 2021 9:49:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:49:03.589 INFO SelectVariants - ------------------------------------------------------------
21:49:03.590 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.2.2.0
21:49:03.590 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
21:49:03.591 INFO SelectVariants - Executing as jingchun@jingchun-VirtualBox on Linux v5.11.0-41-generic amd64
21:49:03.592 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.1+12-Ubuntu-120.04
21:49:03.592 INFO SelectVariants - Start Date/Time: December 13, 2021 at 9:49:03 PM EST
21:49:03.593 INFO SelectVariants - ------------------------------------------------------------
21:49:03.593 INFO SelectVariants - ------------------------------------------------------------
21:49:03.594 INFO SelectVariants - HTSJDK Version: 2.24.1
21:49:03.594 INFO SelectVariants - Picard Version: 2.25.4
21:49:03.603 INFO SelectVariants - Built for Spark Version: 2.4.5
21:49:03.604 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:49:03.604 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:49:03.604 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:49:03.604 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:49:03.605 INFO SelectVariants - Deflater: IntelDeflater
21:49:03.606 INFO SelectVariants - Inflater: IntelInflater
21:49:03.606 INFO SelectVariants - GCS max retries/reopens: 20
21:49:03.607 INFO SelectVariants - Requester pays: disabled
21:49:03.607 INFO SelectVariants - Initializing engine
21:49:03.920 INFO SelectVariants - Shutting down engine
[December 13, 2021 at 9:49:03 PM EST] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=125829120
***********************************************************************

A USER ERROR has occurred: Couldn't read file file:///home/jingchun/GATK/germline_analysis/trio-gdb/. Error was: It isn't a regular file

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

error was： it isn't a regular file.

I don't know what is the cause of this and how to solve it.

Thanks,

Jingchun