v4.2.0.0

 gatk HaplotypeCaller \
-R ${REFERENCE}.fa \
-L ${INTERVAL} \
-I ${BAMPATH} \
-ERC GVCF \
-O $TMPDIR/${SAMPLE}.${INTERVAL}.chrom.g.vcf \
> slurm_out/${SAMPLE}.${INTERVAL}.log 2>&1

Using GATK jar /home/tommathy/apps/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 -jar /home/tommathy/apps/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar HaplotypeCaller -R /projects/jah1_lab/poplar_illumina/Ptrichocarpa_533_v4.0.fa -L Chr03 -I input/sorted-249.bam -ERC GVCF -O /localscratch/532003/sorted-249.Chr03.chrom.g.vcf
10:17:54.813 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/tommathy/apps/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 09, 2022 10:17:54 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:17:54.990 INFO  HaplotypeCaller - ------------------------------------------------------------
10:17:54.990 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0
10:17:54.990 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
10:17:54.990 INFO  HaplotypeCaller - Executing as tommathy@tc108 on Linux v3.10.0-1062.18.1.el7.x86_64 amd64
10:17:54.990 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_322-b06
10:17:54.990 INFO  HaplotypeCaller - Start Date/Time: June 9, 2022 10:17:54 AM EDT
10:17:54.990 INFO  HaplotypeCaller - ------------------------------------------------------------
10:17:54.990 INFO  HaplotypeCaller - ------------------------------------------------------------
10:17:54.991 INFO  HaplotypeCaller - HTSJDK Version: 2.24.0
10:17:54.991 INFO  HaplotypeCaller - Picard Version: 2.25.0
10:17:54.991 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
10:17:54.991 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:17:54.991 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:17:54.991 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:17:54.991 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:17:54.991 INFO  HaplotypeCaller - Deflater: IntelDeflater
10:17:54.991 INFO  HaplotypeCaller - Inflater: IntelInflater
10:17:54.991 INFO  HaplotypeCaller - GCS max retries/reopens: 20
10:17:54.991 INFO  HaplotypeCaller - Requester pays: disabled
10:17:54.991 INFO  HaplotypeCaller - Initializing engine
10:17:55.336 INFO  IntervalArgumentCollection - Processing 21678634 bp from intervals
10:17:55.342 INFO  HaplotypeCaller - Done initializing engine
10:17:55.343 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
10:17:55.352 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
10:17:55.352 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
10:17:55.367 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/tommathy/apps/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:17:55.368 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/tommathy/apps/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
10:17:55.397 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
10:17:55.398 INFO  IntelPairHmm - Available threads: 4
10:17:55.398 INFO  IntelPairHmm - Requested threads: 4
10:17:55.398 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
10:17:55.451 INFO  ProgressMeter - Starting traversal
10:17:55.452 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
10:18:05.473 INFO  ProgressMeter -         Chr03:158559              0.2                   840           5029.9
[Ommitting traversal log for brevity, program completes full traversal of interval]
11:18:21.410 INFO  ProgressMeter -       Chr03:21656885             60.4                114950           1902.1
11:18:24.703 INFO  HaplotypeCaller - 151718 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
94657 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
246375 total reads filtered
11:18:24.703 INFO  ProgressMeter -       Chr03:21676821             60.5                115068           1902.3
11:18:24.703 INFO  ProgressMeter - Traversal complete. Processed 115068 total regions in 60.5 minutes.
11:18:25.027 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
11:18:25.028 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
11:18:25.028 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
11:18:25.028 INFO  HaplotypeCaller - Shutting down engine
[June 9, 2022 11:18:25 AM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 60.50 minutes.
Runtime.totalMemory()=2368208896

I'm currently attempting to use the HaplotypeCaller to genotype pacbio data by chromosome. However, the g.vcf files all end up with just a single variant call that looks like

Chr03   1       .       C       <NON_REF>       .       .       END=21678634    GT:DP:GQ:MIN_DP:PL      0/0:0:0:0:0,0,0

Which appears to be just marking the whole chromosome as NON_REF. I've had success using the HaplotypeCaller on these samples using Illumina reads.