I am trying following commands to generate vcf file from HISAT2 generated alignment .sam file. I tried a lot but I am not able to figure out the issue. please advice.

Command:

./gatk --java-options "-Xmx4g" HaplotypeCaller -R ../sequence.fasta -I ../trt.bam -O ../output.vcf.gz

I also tried command:

./gatk HaplotypeCaller -R ../sequence.fasta -I ../sorted-trt.bam -O ../variants-trt.vcf

MESSAGE from GATK:

Using GATK jar /home/kumarm/allan-work/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 -Xmx4g -jar /home/kumarm/allan-work/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar HaplotypeCaller -R /home/kumarm/allan-work/try/sequence.fasta -I /home/kumarm/allan-work/try/trt.bam -O /home/kumarm/allan-work/try/output.vcf.gz
21:34:11.396 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/kumarm/allan-work/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 12, 2020 9:34:11 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:34:11.562 INFO HaplotypeCaller - ------------------------------------------------------------
21:34:11.563 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.7.0
21:34:11.563 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
21:34:11.563 INFO HaplotypeCaller - Executing as kumarm@microbiome on Linux v4.15.0-99-generic amd64
21:34:11.563 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.1+13-LTS
21:34:11.563 INFO HaplotypeCaller - Start Date/Time: May 12, 2020 at 9:34:11 PM CDT
21:34:11.563 INFO HaplotypeCaller - ------------------------------------------------------------
21:34:11.563 INFO HaplotypeCaller - ------------------------------------------------------------
21:34:11.564 INFO HaplotypeCaller - HTSJDK Version: 2.21.2
21:34:11.564 INFO HaplotypeCaller - Picard Version: 2.21.9
21:34:11.564 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:34:11.564 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:34:11.565 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:34:11.565 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:34:11.565 INFO HaplotypeCaller - Deflater: IntelDeflater
21:34:11.565 INFO HaplotypeCaller - Inflater: IntelInflater
21:34:11.565 INFO HaplotypeCaller - GCS max retries/reopens: 20
21:34:11.565 INFO HaplotypeCaller - Requester pays: disabled
21:34:11.565 INFO HaplotypeCaller - Initializing engine
21:34:11.726 INFO HaplotypeCaller - Done initializing engine
21:34:11.732 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
21:34:11.739 INFO HaplotypeCaller - Shutting down engine
[May 12, 2020 at 9:34:11 PM CDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2113929216
java.lang.IllegalArgumentException: samples cannot be empty
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:727)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.<init>(ReferenceConfidenceModel.java:119)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:223)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(HaplotypeCallerEngine.java:166)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:196)
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)