REQUIRED for all errors and issues:
a) GATK version used: v4.2.5.0
b) Exact command used:  I used SelectVariants to generate one vcf file per sample and then used: 

FastaAlternateReferenceMaker -R genomic.fna -O sample.fasta -L chromosome -V sample.vcf

c) Entire program log:

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 user/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar 
FastaAlternateReferenceMaker -R genomic.fna -O sample.fasta -L chromosome -V sample.vcf
09:02:24.157 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/user/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 17, 2023 9:02:24 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
09:02:24.270 INFO  FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO  FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.2.5.0
09:02:24.271 INFO  FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/
09:02:24.271 INFO  FastaAlternateReferenceMaker - Executing as user@compute-1-1734.local on Linux v3.10.0-693.5.2.el7.x86_64 amd64
09:02:24.271 INFO  FastaAlternateReferenceMaker - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
09:02:24.271 INFO  FastaAlternateReferenceMaker - Start Date/Time: March 17, 2023 9:02:24 AM CDT
09:02:24.271 INFO  FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO  FastaAlternateReferenceMaker - ------------------------------------------------------------
09:02:24.271 INFO  FastaAlternateReferenceMaker - HTSJDK Version: 2.24.1
09:02:24.272 INFO  FastaAlternateReferenceMaker - Picard Version: 2.25.4
09:02:24.272 INFO  FastaAlternateReferenceMaker - Built for Spark Version: 2.4.5
09:02:24.272 INFO  FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:02:24.272 INFO  FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:02:24.272 INFO  FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:02:24.272 INFO  FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:02:24.272 INFO  FastaAlternateReferenceMaker - Deflater: IntelDeflater
09:02:24.272 INFO  FastaAlternateReferenceMaker - Inflater: IntelInflater
09:02:24.272 INFO  FastaAlternateReferenceMaker - GCS max retries/reopens: 20
09:02:24.272 INFO  FastaAlternateReferenceMaker - Requester pays: disabled
09:02:24.272 INFO  FastaAlternateReferenceMaker - Initializing engine
09:02:24.751 INFO  FeatureManager - Using codec VCFCodec to read file file:///sample.vcf
09:02:24.783 INFO  IntervalArgumentCollection - Processing 49793703 bp from intervals
09:02:24.786 INFO  FastaAlternateReferenceMaker - Done initializing engine
09:02:24.794 INFO  ProgressMeter - Starting traversal
09:02:24.794 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Bases Processed     Bases/Minute
09:02:34.798 INFO  ProgressMeter -  chromosome              0.2              32033000      192159568.1
09:02:40.564 INFO  ProgressMeter -  chromosome              0.3              49793703      189449726.1
09:02:40.565 INFO  ProgressMeter - Traversal complete. Processed 49793703 total bases in 0.3 minutes.
09:02:41.668 INFO  FastaAlternateReferenceMaker - Shutting down engine
[March 17, 2023 9:02:41 AM CDT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=6493831168