REQUIRED for all errors and issues:
a) GATK version used: gatk-4.2.6.1
b) Exact command used: 

gatk --java-options "-Xms80G -Xmx80G -XX:-UseGCOverheadLimit -XX:+UseParallelGC -XX:ParallelGCThreads=16" Mutect2 \
-native-pair-hmm-threads 16 \
-R $GENOME/GRCh38_p13.fa \
-I $OUTPUT_GATK/${lib}"_recalibrated.bam" \
-pon $SITES/Mutect2_1000g_pon.hg38.vcf.gz \
--germline-resource $SITES/af-only-gnomad.hg38.vcf.gz \
--read-filter NotSecondaryAlignmentReadFilter \
--read-filter NotSupplementaryAlignmentReadFilter \
-L $ONCO_BED \
-O $OUTPUT_GATK/${lib}".vcf.gz" \
-bamout $OUTPUT_GATK/${lib}"_mutect2.bam"

c) Entire program log:
16:11:25.140 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:11:25.461 INFO  Mutect2 - ------------------------------------------------------------
16:11:25.462 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.6.1
16:11:25.462 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
16:11:25.463 INFO  Mutect2 - Executing as sassou@node124 on Linux v3.10.0-1160.el7.x86_64 amd64
16:11:25.463 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_262-b10
16:11:25.464 INFO  Mutect2 - Start Date/Time: January 26, 2023 4:11:25 PM CET
16:11:25.464 INFO  Mutect2 - ------------------------------------------------------------
16:11:25.464 INFO  Mutect2 - ------------------------------------------------------------
16:11:25.464 INFO  Mutect2 - HTSJDK Version: 2.24.1
16:11:25.464 INFO  Mutect2 - Picard Version: 2.27.1
16:11:25.465 INFO  Mutect2 - Built for Spark Version: 2.4.5
16:11:25.465 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:11:25.465 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:11:25.465 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:11:25.465 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:11:25.465 INFO  Mutect2 - Deflater: IntelDeflater
16:11:25.465 INFO  Mutect2 - Inflater: IntelInflater
16:11:25.465 INFO  Mutect2 - GCS max retries/reopens: 20
16:11:25.466 INFO  Mutect2 - Requester pays: disabled
16:11:25.466 INFO  Mutect2 - Initializing engine
16:11:26.353 INFO  FeatureManager - Using codec VCFCodec to read file file:////GRCh38_p13/Mutect2_1000g_pon.hg38.vcf.gz
16:11:26.717 INFO  FeatureManager - Using codec VCFCodec to read file file:////GRCh38_p13/af-only-gnomad.hg38.vcf.gz
16:11:27.125 INFO  FeatureManager - Using codec BEDCodec to read file file:////REDA/REDA.bed
16:11:27.176 INFO  IntervalArgumentCollection - Processing 102791 bp from intervals
16:11:27.290 INFO  Mutect2 - Done initializing engine
16:11:27.368 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
16:11:27.370 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
16:11:27.448 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
16:11:27.461 INFO  IntelPairHmm - Available threads: 1
16:11:27.461 INFO  IntelPairHmm - Requested threads: 16
16:11:27.461 WARN  IntelPairHmm - Using 1 available threads, but 16 were requested
16:11:27.461 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
16:11:27.589 INFO  ProgressMeter - Starting traversal
16:11:27.589 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
16:11:54.454 INFO  ProgressMeter -        chr2:25235659              0.4                    20             44.7
16:12:11.521 INFO  ProgressMeter -        chr2:25245332              0.7                    30             41.0
16:12:42.043 INFO  ProgressMeter -       chr2:197402921              1.2                    50             40.3
16:13:12.839 INFO  ProgressMeter -       chr3:128486291              1.8                    60             34.2
16:13:26.717 INFO  ProgressMeter -       chr4:105275608              2.0                    90             45.3
16:13:42.150 INFO  ProgressMeter -       chr5:177512483              2.2                   100             44.6
16:14:10.866 INFO  ProgressMeter -       chr5:177516075              2.7                   110             40.4
16:14:33.803 INFO  ProgressMeter -       chr7:102111676              3.1                   120             38.7
16:14:44.959 INFO  ProgressMeter -       chr7:102196897              3.3                   130             39.5
16:15:02.405 INFO  ProgressMeter -       chr7:102227466              3.6                   140             39.1
16:15:12.890 INFO  ProgressMeter -       chr9:130862715              3.8                   180             47.9
16:15:25.842 INFO  ProgressMeter -       chr11:32392636              4.0                   200             50.4
16:15:38.416 INFO  ProgressMeter -        chr17:1660393              4.2                   250             59.8
16:15:58.731 INFO  ProgressMeter -        chr17:7674145              4.5                   290             64.2
16:16:22.600 INFO  ProgressMeter -        chr17:7676492              4.9                   300             61.0
16:16:35.000 INFO  ProgressMeter -       chr17:31182479              5.1                   310             60.5
16:16:51.587 INFO  ProgressMeter -       chr17:31232874              5.4                   340             63.0
16:17:15.035 INFO  ProgressMeter -       chr17:31261654              5.8                   350             60.4
16:17:32.244 INFO  ProgressMeter -       chr17:31350135              6.1                   370             60.9
16:17:59.031 INFO  ProgressMeter -       chr17:60600376              6.5                   380             58.2
16:18:13.944 INFO  ProgressMeter -       chr19:33301798              6.8                   400             59.1
16:18:33.509 INFO  ProgressMeter -       chr20:32434714              7.1                   420             59.2
16:18:59.833 INFO  ProgressMeter -       chr21:34892882              7.5                   440             58.4
16:19:13.799 INFO  ProgressMeter -        chrX:40063578              7.8                   470             60.5
16:19:34.457 INFO  ProgressMeter -       chrX:124022565              8.1                   490             60.4
16:19:44.934 INFO  ProgressMeter -       chrX:130013501              8.3                   530             63.9
16:20:10.057 INFO  ProgressMeter -       chrX:130015826              8.7                   540             62.0
16:20:17.924 INFO  Mutect2 - 2609 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
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: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
2609 total reads filtered
16:20:17.924 INFO  ProgressMeter -       chrX:134413756              8.8                   563             63.7
16:20:17.925 INFO  ProgressMeter - Traversal complete. Processed 563 total regions in 8.8 minutes.
16:20:17.976 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.227637305
16:20:17.976 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 346.50865353200004
16:20:17.976 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 13.21 sec
16:20:19.154 INFO  Mutect2 - Shutting down engine
[January 26, 2023 4:20:19 PM CET] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 8.90 minutes.
Runtime.totalMemory()=65856339968
Tool returned:
SUCCESS
Using GATK jar /GATK/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

Mutect2 failed when the mutation is located on a secondary alignment, see below:

M02792:126:000000000-K9RHL:1:1114:12346:24983   163     chr21   43104253        0       147M    =       43104346        240     TTAACTGTCTTTGAAAAGAACATGAAGTTTTTATAATTTACATGAAAAAAAGGCAAACAAACCTGGCTAAACGTCGGTTTATTGTGCAACCGAGAGCACCTGTCTCCATGACGACATGCTCCAATTTTGAAATAAAATGAACAGTTG  BEDHBFFDGFEEDEGGHHFIDECKFJGEFGFEBEBJEFEBDEEKGJJJJHGHDIEJJEEJJDEIKIFGBJJDBEHBHDFFBEEKFGFFJDEBFHFHGEFHHKEHHHHEELFDBFFEDLFHIHEJEFFFKFJKFBJJJDKGKFEGEFD     XA:Z:chr21,+6495931,147M,0;     ZA:Z:CGCT   ZB:Z:CCGT        BC:Z:5  MD:Z:147        RG:Z:SAD190004_S5       NM:i:0  AS:i:147        XS:i:147        QX:Z:CCB ABC    RX:Z:CGC-CCG    xc:i:1  zd:Z:   xm:i:1 M02792:126:000000000-
K9RHL:1:1114:12346:24983   83      chr21   43104346        0       147M    =       43104253        -240    GAGCACCTGTCTCCATGACGACATGCTCCAATTTTGAAATAAAATGAACAGTTGACTCTGTAAGGGAAAATGAGAGCTGATTATTTTGCTGGGAAGATATCAAACACATGGAATATGTCAGCAGCATGACATACACTATCAAATTAC  HHFLEHGEFFFGIKFEGDEHEKEEFGGIKGEIJJEHEFEBFFGEEHFFKHEJEHEGGGEDBGHHHHFGGEFHHGIFHFHEJCEJJJEFHFIHHFIHEBEHKGFFLEKEEHHGEBEEEHLHGLHFLEEHEDDCDCDHCDEHDECHCCD     XA:Z:chr21,-6496024,147M,0;     ZA:Z:CGCT   ZB:Z:CCGT        BC:Z:5  MD:Z:147        RG:Z:SAD190004_S5       NM:i:0  AS:i:147        XS:i:147        QX:Z:CCB ABC    RX:Z:CGC-CCG    xc:i:1  zd:Z:   xm:i:1