REQUIRED for all errors and issues:
a) GATK version used: gatk/4.2.6.1-i66r6j
b) Exact command used: gatk HaplotypeCaller -R /C_glabrata_CBS138.fasta -I ${i}.mark.bam -O //Variants/${i}_rawvariants.vcf
c) Entire program log:

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /storage/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gatk-4.2.6.1-i66r6jtxdqbv44rewzcahc5ungj7bkar/bin/gatk-package-4.2.6.1-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 /storage/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gatk-4.2.6.1-i66r6jtxdqbv44rewzcahc5ungj7bkar/bin/gatk-package-4.2.6.1-local.jar HaplotypeCaller -R /storage/home/hcoda1/8/mgranada3/scratch/Reference/C_glabrata_CBS138_current_chromosomes.fasta -I FR04_YPD_SC_0_S1_rg.mark.bam -O /storage/home/hcoda1/8/mgranada3/scratch/Variants/FR04_YPD_SC_0_S1_rg_rawvariants.vcf
11:51:09.615 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/storage/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gatk-4.2.6.1-i66r6jtxdqbv44rewzcahc5ungj7bkar/bin/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:51:09.730 INFO  HaplotypeCaller - ------------------------------------------------------------
11:51:09.730 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.6.1
11:51:09.730 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
11:51:09.730 INFO  HaplotypeCaller - Executing as mgranada3@atl1-1-02-019-35-2.pace.gatech.edu on Linux v3.10.0-1160.49.1.el7.x86_64 amd64
11:51:09.731 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_392-b08
11:51:09.731 INFO  HaplotypeCaller - Start Date/Time: February 9, 2024 11:51:09 AM EST
11:51:09.731 INFO  HaplotypeCaller - ------------------------------------------------------------
11:51:09.731 INFO  HaplotypeCaller - ------------------------------------------------------------
11:51:09.731 INFO  HaplotypeCaller - HTSJDK Version: 2.24.1
11:51:09.731 INFO  HaplotypeCaller - Picard Version: 2.27.1
11:51:09.731 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
11:51:09.731 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:51:09.732 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:51:09.732 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:51:09.732 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:51:09.732 INFO  HaplotypeCaller - Deflater: IntelDeflater
11:51:09.732 INFO  HaplotypeCaller - Inflater: IntelInflater
11:51:09.732 INFO  HaplotypeCaller - GCS max retries/reopens: 20
11:51:09.732 INFO  HaplotypeCaller - Requester pays: disabled
11:51:09.732 INFO  HaplotypeCaller - Initializing engine
11:51:09.736 INFO  HaplotypeCaller - Shutting down engine
[February 9, 2024 11:51:09 AM EST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2199912448
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A USER ERROR has occurred: Fasta dict file file:///storage/home/hcoda1/8/mgranada3/scratch/Reference/C_glabrata_CBS138_current_chromosomes.dict for reference file:///storage/home/hcoda1/8/mgranada3/scratch/Reference/C_glabrata_CBS138_current_chromosomes.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
---------------------------------------
Begin Slurm Epilog: Feb-09-2024 11:51:09
Job ID:        4908811
Array Job ID:  _4294967294
User ID:       mgranada3
Account:       gts-rrosenzweig3
Job name:      SCrawvariants
Resources:     cpu=48,mem=384G,node=2
Rsrc Used:     cput=00:46:24,vmem=301016K,walltime=00:00:58,mem=181380K,energy_used=0
Partition:     cpu-small
QOS:           inferno
Nodes:         atl1-1-02-019-35-2,atl1-1-02-019-36-2