REQUIRED for all errors and issues:
a) GATK version used: 4.2.6.0
b) Exact command used: /home/703404669/gatk-4.2.6.0/gatk --java-options "-Xmx4g" HaplotypeCaller --input HG7H5Aligned.sortedByCoord.out.ar.bam --reference /usr/local/share/hg38/hg38.fa -O HGFLY.g.vcf.gz -ERC GVCF
c) Entire program log:
Using GATK jar /home/703404669/gatk-4.2.6.0/gatk-package-4.2.6.0-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/703404669/gatk-4.2.6.0/gatk-package-4.2.6.0-local.jar HaplotypeCaller --input HG7H5Aligned.sortedByCoord.out.ar.bam --reference /usr/local/share/hg38/hg38.fa -O HGFLY.g.vcf.gz -ERC GVCF
10:47:55.924 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/703404669/gatk-4.2.6.0/gatk-package-4.2.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:47:56.013 INFO  HaplotypeCaller - ------------------------------------------------------------
10:47:56.013 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.6.0
10:47:56.013 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
10:47:56.013 INFO  HaplotypeCaller - Executing as 703404669@BioITUtil2.sanfordhealth.org on Linux v4.18.0-372.19.1.el8_6.x86_64 amd64
10:47:56.013 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_342-b07
10:47:56.014 INFO  HaplotypeCaller - Start Date/Time: August 5, 2022 10:47:55 AM CDT
10:47:56.014 INFO  HaplotypeCaller - ------------------------------------------------------------
10:47:56.014 INFO  HaplotypeCaller - ------------------------------------------------------------
10:47:56.014 INFO  HaplotypeCaller - HTSJDK Version: 2.24.1
10:47:56.014 INFO  HaplotypeCaller - Picard Version: 2.27.1
10:47:56.014 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
10:47:56.014 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:47:56.014 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:47:56.014 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:47:56.014 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:47:56.014 INFO  HaplotypeCaller - Deflater: IntelDeflater
10:47:56.014 INFO  HaplotypeCaller - Inflater: IntelInflater
10:47:56.014 INFO  HaplotypeCaller - GCS max retries/reopens: 20
10:47:56.014 INFO  HaplotypeCaller - Requester pays: disabled
10:47:56.015 INFO  HaplotypeCaller - Initializing engine
10:47:56.285 INFO  HaplotypeCaller - Done initializing engine
10:47:56.287 INFO  HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled
10:47:56.296 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
10:47:56.297 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
10:47:56.308 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/703404669/gatk-4.2.6.0/gatk-package-4.2.6.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:47:56.309 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/703404669/gatk-4.2.6.0/gatk-package-4.2.6.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
10:47:56.327 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
10:47:56.327 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
10:47:56.327 INFO  IntelPairHmm - Available threads: 10
10:47:56.327 INFO  IntelPairHmm - Requested threads: 4
10:47:56.328 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
10:47:56.354 INFO  ProgressMeter - Starting traversal
10:47:56.355 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
10:47:56.364 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
10:47:56.364 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
10:47:56.365 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
10:47:56.365 INFO  HaplotypeCaller - Shutting down engine
[August 5, 2022 10:47:56 AM CDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1346895872
java.nio.BufferUnderflowException
    at java.nio.ByteBuffer.get(ByteBuffer.java:696)
    at java.nio.DirectByteBuffer.get(DirectByteBuffer.java:284)
    at java.nio.ByteBuffer.get(ByteBuffer.java:723)
    at htsjdk.samtools.MemoryMappedFileBuffer.readBytes(MemoryMappedFileBuffer.java:34)
    at htsjdk.samtools.AbstractBAMFileIndex.readBytes(AbstractBAMFileIndex.java:439)
    at htsjdk.samtools.AbstractBAMFileIndex.verifyIndexMagicNumber(AbstractBAMFileIndex.java:376)
    at htsjdk.samtools.AbstractBAMFileIndex.<init>(AbstractBAMFileIndex.java:70)
    at htsjdk.samtools.AbstractBAMFileIndex.<init>(AbstractBAMFileIndex.java:64)
    at htsjdk.samtools.DiskBasedBAMFileIndex.<init>(DiskBasedBAMFileIndex.java:46)
    at htsjdk.samtools.BAMFileReader.getIndex(BAMFileReader.java:419)
    at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:931)
    at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612)
    at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:550)
    at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:417)
    at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:130)
    at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:69)
    at org.broadinstitute.hellbender.engine.ReadsPathDataSource.prepareIteratorsForTraversal(ReadsPathDataSource.java:412)
    at org.broadinstitute.hellbender.engine.ReadsPathDataSource.iterator(ReadsPathDataSource.java:336)
    at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
    at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:86)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:188)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    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)

I have used STAR to align some whole exome sequencing files:

    STAR --readFilesCommand zcat --runThreadN 4 --genomeDir /usr/local/share/hg38 --outFileNamePrefix HGFLY --readFilesIn AGKD01_CKDN220004842-1A_HGFLYDSX3_L1_1.fq.gz AGKD01_CKDN220004842-1A_HGFLYDSX3_L1_2.fq.gz --outSAMtype BAM SortedByCoordinate

but when I run haplotypeCaller in the next step:

    ~/gatk-4.2.6.0/gatk --java-options "-Xmx4g" HaplotypeCaller --input HGFLYAligned.sortedByCoord.out.bam --reference /usr/local/share/hg38/hg38.fa -O HGFLY.g.vcf.gz -ERC GVCF

I get an error: 

    A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.

but when I try to view the samples `samtools view -H HGFLYAligned.sortedByCoord.out.bam | grep RG`  I get none.

I have found similar errors reported, https://gatk.broadinstitute.org/hc/en-us/community/posts/360075892511-emit-ref-confidence-error but I don't see a solution to my problem there.

It seems that my alignment produced no sample names, and I don't see how STAR can output sample names.

A sample view of my bam file:

    A00564:479:HGFLYDSX3:1:2420:11686:10708    163    chr1    10001    255    6S108M36S    =    10191    
    170948    TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
    TAACCCTAACCCTAACCCGAAACCCAAAACCCAAAACCCGAAACCCAAAACCCA    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF
    FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFF,F::FFFF:F:F,FFFFF,,FF,:,,,FFF:F,,F::,:F,F,F,:F,    
    NH:i:1    HI:i:1    AS:i:200    nM:i:10
    A00564:479:HGFLYDSX3:1:2573:2889:29669    163    chr1    10001    255    1S113M36S    =    10005    
    104    CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
    CTAACCCTAACCCAAACCCTAACCCTAACCCTAAACCTAACCCTCACCCTAACC    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF
    FFFFFF::FFFFFFFFFFF,FFFFFFF,FFF,FFFF,,::FFF,FFFFF,,FFFF,FFFFF,:FFF,,F:FF,:F,FFF,,F,FF,FFFFF,,,F,F,,,,F    
    NH:i:1    HI:i:1    AS:i:207    nM:i:2
    A00564:479:HGFLYDSX3:1:2140:5656:8844    163    chr1    10004    3    106M44S    =    10004    110    
    CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC
    CAGCGCCAGAGCCTAGGCGGGGGCCTACGGCTGGGCCGGAGGGTGG    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    FFFFFFFFFFFFFFFF:FFFFFFFF:F::FF,FF,FFFF:,,F,::,,,,,,,,:,,,,:,,,,,,,,,,,,,:,,:,,,,,,,,,,,,,,:,,    NH:i:2    
    HI:i:1    AS:i:206    nM:i:4

I posted on BioStars, but didn't get an answer.

How can I call haplotypes/variants? Thanks for your help