I'm interested in running HaplotypeCaller, but first I've been going through the best practices pipeline (Data pre-processing for variant discovery). I'm encountering an error when running GATK 4.4.0 and 4.6.0, specifically with the MergeBamAlignment tool. Below some details:

REQUIRED for all errors and issues:
a) GATK version used:

gatk 4.4.0.0 and gatk 4.6.0.0

b) Exact command used:

gatk MergeBamAlignment --ALIGNED gh37.bam --UNMAPPED unmapped_gh37.bam -O merged_gh37.bam -R Marasmius_tenuissimus_GH37.scaffolds.fa --SORT_ORDER coordinate --CREATE_INDEX true --VALIDATION_STRINGENCY LENIENT --MAX_GAPS -1

 
c) Entire program log:

Using GATK jar /project/software/el9/apps/gatk/4.4.0.0/gatk-package-4.4.0.0-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 /project/software/el9/apps/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar MergeBamAlignment --ALIGNED gh37.bam --UNMAPPED unmapped_gh37.bam -O merged_gh37.bam -R Marasmius_tenuissimus_GH37.scaffolds.fa --SORT_ORDER coordinate --CREATE_INDEX true --VALIDATION_STRINGENCY LENIENT --MAX_GAPS -1
11:16:24.968 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/project/software/el9/apps/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:16:25.092 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/gabdiel.yulfosoto/libgkl_compression6503066253920356115.so: /tmp/gabdiel.yulfosoto/libgkl_compression6503066253920356115.so: failed to map segment from shared object)
11:16:25.093 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/project/software/el9/apps/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:16:25.099 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/gabdiel.yulfosoto/libgkl_compression4616878669524355092.so: /tmp/gabdiel.yulfosoto/libgkl_compression4616878669524355092.so: failed to map segment from shared object)
[Wed Sep 11 11:16:25 CDT 2024] MergeBamAlignment --UNMAPPED_BAM unmapped_gh37.bam --ALIGNED_BAM gh37.bam --OUTPUT merged_gh37.bam --MAX_INSERTIONS_OR_DELETIONS -1 --SORT_ORDER coordinate --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE Marasmius_tenuissimus_GH37.scaffolds.fa --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed Sep 11 11:16:25 CDT 2024] Executing as gabdiel.yulfosoto@ceres19-compute-60.ceres.scinet.usda.gov on Linux 5.14.0-284.82.1.el9_2.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.11+9; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:4.4.0.0
INFO    2024-09-11 11:16:25     SamAlignmentMerger      Processing SAM file(s): [gh37.bam]
11:16:25.128 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
11:16:25.158 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
[Wed Sep 11 11:16:25 CDT 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=285212672
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///90daydata/spcl-pathogen-genomes/GYS/snp_calling/Marasmius_tenuissimus_GH37.scaffolds.fa
        at htsjdk.variant.utils.SAMSequenceDictionaryExtractor$TYPE$1.extractDictionary(SAMSequenceDictionaryExtractor.java:58)
        at htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(SAMSequenceDictionaryExtractor.java:170)
        at picard.sam.SamAlignmentMerger.getDictionaryForMergedBam(SamAlignmentMerger.java:192)
        at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:384)
        at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:181)
        at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:368)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
        at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
        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)