REQUIRED for all errors and issues:
a) GATK version used:gatk-4.2.0.0 
b) Exact command used:

#!/bin/bash
#$ -cwd
#$ -l h_rt=24:00:00
#$ -pe smp 1
#$ -l h_vmem=32G
#$ -N Mutect2_WES40
#$ -o Mutect2_WES40.out
#$ -e Mutect2_WES40.err
#$ -binding linear:1
#$ -M imonga@broadinstitute.org
#$ -m bea

source /broad/software/scripts/useuse
use .anaconda3-5.3.1
#conda activate scrnatools
#use Java-1.8
use Samtools
use UGER
use Java-17
use .gatk-4.2.0.0
REFERENCE="/ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/Homo_sapiens_assembly38.fasta"

# Define the path to the directory containing your paired-end FASTQ files
FASTQ_DIR="/broad/hptmp/imonga/Tocheva_data/bulk_exome"
# Specify the full path to samtools
#SAMTOOLS="/ahg/regevdata/projects/ICA_Lung/Isha/conda/envs/scrnatools/bin/samtools"
SAMTOOLS="/broad/software/free/Linux/redhat_7_x86_64/pkgs/samtools/samtools_1.9/bin/samtools"
BCFTOOLS="/broad/software/free/Linux/redhat_7_x86_64/pkgs/bcftools/bcftools_1.9/bin/bcftools"
export GATK_PATH="/broad/software/free/Linux/redhat_7_x86_64/pkgs/gatk_4.2.0.0/gatk"

OUTPUT_DIR="/broad/hptmp/imonga/Tocheva_data/bulk_exome"  # Change this to the desired output directory
OUTPUT_DIR1="/broad/hptmp/imonga/Tocheva_data/bulk_exome/hg38_bams/fixmate_bams"
BAM_DIR="/broad/hptmp/imonga/Tocheva_data/bulk_exome/hg38_bams/fixmate_bams/"
pon_DIR="/ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/hg38_pon/"

gnomad_DIR="/ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/"

gatk Mutect2 -R $REFERENCE  -I "$BAM_DIR/Addedsample-WES40.sorted_markdup.bam" --germline-resource  "$gnomad_DIR/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz" --panel-of-normals "$pon_DIR/gatk4_mutect2_4136_pon.vcf.gz" -O  "$BAM_DIR/Addedsample-WES40.single_sample.vcf.gz" --tmp-dir /broad/hptmp/imonga/

 
c) Entire program log:
/var/spool/uger-8.5.5/ugertmp-c009/job_scripts/41575977: line 15: conda: command not found
Using GATK jar /broad/software/free/Linux/redhat_7_x86_64/pkgs/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 /broad/software/free/Linux/redhat_7_x86_64/pkgs/gatk_4.2.0.0/gatk-package-4.2.0.0-local.jar Mutect2 -R /ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/Homo_sapiens_assembly38.fasta -I /broad/hptmp/imonga/Tocheva_data/bulk_exome/hg38_bams/fixmate_bams//Addedsample-WES40.sorted_markdup.bam --germline-resource /ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38//gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz --panel-of-normals /ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/hg38_pon//gatk4_mutect2_4136_pon.vcf.gz -O /broad/hptmp/imonga/Tocheva_data/bulk_exome/hg38_bams/fixmate_bams//Addedsample-WES40.single_sample.vcf.gz --tmp-dir /broad/hptmp/imonga/ --ignore-itr-artifacts true --max-prob-propagation-distance 100000
20:32:40.051 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/broad/software/free/Linux/redhat_7_x86_64/pkgs/gatk_4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 05, 2023 8:32:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
20:32:40.492 INFO  Mutect2 - ------------------------------------------------------------
20:32:40.492 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.0.0
20:32:40.492 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
20:32:40.495 INFO  Mutect2 - Executing as imonga@ugertmp-c009.broadinstitute.org on Linux v3.10.0-1160.102.1.el7.x86_64 amd64
20:32:40.495 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_345-b01
20:32:40.496 INFO  Mutect2 - Start Date/Time: December 5, 2023 8:32:40 PM UTC
20:32:40.496 INFO  Mutect2 - ------------------------------------------------------------
20:32:40.496 INFO  Mutect2 - ------------------------------------------------------------
20:32:40.496 INFO  Mutect2 - HTSJDK Version: 2.24.0
20:32:40.496 INFO  Mutect2 - Picard Version: 2.25.0
20:32:40.496 INFO  Mutect2 - Built for Spark Version: 2.4.5
20:32:40.496 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:32:40.497 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:32:40.497 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:32:40.497 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:32:40.497 INFO  Mutect2 - Deflater: IntelDeflater
20:32:40.497 INFO  Mutect2 - Inflater: IntelInflater
20:32:40.497 INFO  Mutect2 - GCS max retries/reopens: 20
20:32:40.497 INFO  Mutect2 - Requester pays: disabled
20:32:40.497 INFO  Mutect2 - Initializing engine
20:32:41.866 INFO  FeatureManager - Using codec VCFCodec to read file file:///ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/hg38_pon/gatk4_mutect2_4136_pon.vcf.gz
20:32:42.446 INFO  FeatureManager - Using codec VCFCodec to read file file:///ahg/regevdata/projects/ICA_Lung/Isha/LabCode_demux/exome_gatk/hg38/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz
20:32:43.022 INFO  Mutect2 - Done initializing engine
20:32:43.456 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/broad/software/free/Linux/redhat_7_x86_64/pkgs/gatk_4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
20:32:43.511 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/broad/software/free/Linux/redhat_7_x86_64/pkgs/gatk_4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:32:43.617 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
20:32:43.617 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:32:43.618 INFO  IntelPairHmm - Available threads: 1
20:32:43.618 INFO  IntelPairHmm - Requested threads: 4
20:32:43.618 WARN  IntelPairHmm - Using 1 available threads, but 4 were requested
20:32:43.618 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:32:43.806 INFO  ProgressMeter - Starting traversal
20:32:43.807 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
20:32:54.902 INFO  ProgressMeter -          chr1:186691              0.2                   660           3569.2
20:33:06.304 INFO  ProgressMeter -          chr1:844749              0.4                  2930           7814.4
20:33:18.979 INFO  ProgressMeter -          chr1:866573              0.6                  3010           5134.8
20:33:30.745 INFO  ProgressMeter -          chr1:880313              0.8                  3060           3911.5
20:33:44.015 INFO  ProgressMeter -          chr1:943390              1.0                  3300           3288.6
20:33:55.251 INFO  ProgressMeter -          chr1:954718              1.2                  3350           2813.4
20:34:06.962 INFO  ProgressMeter -          chr1:984271              1.4                  3480           2511.0
20:34:18.077 INFO  ProgressMeter -         chr1:1060036              1.6                  3800           2418.6
20:34:28.404 INFO  ProgressMeter -         chr1:1094283              1.7                  3940           2260.1
20:34:39.182 INFO  ProgressMeter -         chr1:1185574              1.9                  4300           2236.2
20:34:49.223 INFO  ProgressMeter -         chr1:1204704              2.1                  4380           2095.4
20:35:01.027 INFO  ProgressMeter -         chr1:1222264              2.3                  4450           1945.8
20:35:13.238 INFO  ProgressMeter -         chr1:1240189              2.5                  4520           1814.9
20:35:23.497 INFO  ProgressMeter -         chr1:1298527              2.7                  4760           1788.5
20:35:35.217 INFO  ProgressMeter -         chr1:1340224              2.9                  4940           1729.2
20:35:45.247 INFO  ProgressMeter -         chr1:1436832              3.0                  5320           1759.3
20:35:56.293 INFO  ProgressMeter -         chr1:1529580              3.2                  5690           1773.6
20:36:06.488 INFO  ProgressMeter -         chr1:1577703              3.4                  5880           1740.7
20:36:17.162 INFO  ProgressMeter -         chr1:1627553              3.6                  6080           1709.8
20:36:27.649 INFO  ProgressMeter -         chr1:1706071              3.7                  6400           1715.5
20:36:37.754 INFO  ProgressMeter -         chr1:1847883              3.9                  6960           1785.0
20:36:47.866 INFO  ProgressMeter -         chr1:2047121              4.1                  7750           1905.3
20:36:57.887 INFO  ProgressMeter -         chr1:2214889              4.2                  8410           1986.0
20:37:07.973 INFO  ProgressMeter -         chr1:3305986              4.4                 12350           2805.1
20:37:18.048 INFO  ProgressMeter -         chr1:3399607              4.6                 12700           2778.6
20:37:28.413 INFO  ProgressMeter -         chr1:3532533              4.7                 13230           2789.1
20:37:38.413 INFO  ProgressMeter -         chr1:3703209              4.9                 13890           2828.9
20:37:48.469 INFO  ProgressMeter -         chr1:3861806              5.1                 14500           2855.6
20:37:58.576 INFO  ProgressMeter -         chr1:5808448              5.2                 21620           4121.1
20:38:08.613 INFO  ProgressMeter -         chr1:6046504              5.4                 22540           4163.7
20:38:18.807 INFO  ProgressMeter -         chr1:6180085              5.6                 23070           4131.9
20:38:29.203 INFO  ProgressMeter -         chr1:6360981              5.8                 23780           4130.9
20:38:39.327 INFO  ProgressMeter -         chr1:6458931              5.9                 24170           4079.1
20:38:49.835 INFO  ProgressMeter -         chr1:6546195              6.1                 24530           4021.0
20:38:59.861 INFO  ProgressMeter -         chr1:7303995              6.3                 27410           4373.3
20:39:09.898 INFO  ProgressMeter -         chr1:7877786              6.4                 29590           4598.4
20:39:20.631 INFO  ProgressMeter -         chr1:8361339              6.6                 31400           4747.7
20:39:30.938 INFO  ProgressMeter -         chr1:8938309              6.8                 33560           4945.8
20:39:41.480 INFO  ProgressMeter -         chr1:9265190              7.0                 34820           5002.0
20:39:51.824 INFO  ProgressMeter -         chr1:9609867              7.1                 36160           5069.0
20:40:01.886 INFO  ProgressMeter -         chr1:9874969              7.3                 37180           5092.2
20:40:12.088 INFO  ProgressMeter -        chr1:10312573              7.5                 38820           5195.8
20:40:22.555 INFO  ProgressMeter -        chr1:10557746              7.6                 39740           5197.6
20:40:33.073 INFO  ProgressMeter -        chr1:10946202              7.8                 41200           5267.8
20:40:43.690 INFO  ProgressMeter -        chr1:11075452              8.0                 41720           5216.3
20:40:53.720 INFO  ProgressMeter -        chr1:11528727              8.2                 43430           5318.9
20:41:04.193 INFO  ProgressMeter -        chr1:11678198              8.3                 44000           5275.9
20:41:14.522 INFO  ProgressMeter -        chr1:11792909              8.5                 44470           5224.4
20:41:24.534 INFO  ProgressMeter -        chr1:11938523              8.7                 45030           5188.5
20:41:34.587 INFO  ProgressMeter -        chr1:12215858              8.8                 46120           5213.5
20:41:44.686 INFO  ProgressMeter -        chr1:12727727              9.0                 48010           5325.8
20:41:54.771 INFO  ProgressMeter -        chr1:13382704              9.2                 50290           5476.6
20:42:04.772 INFO  ProgressMeter -        chr1:14906957              9.3                 55870           5975.8
20:42:14.863 INFO  ProgressMeter -        chr1:15299066              9.5                 57330           6023.6
20:42:25.000 INFO  ProgressMeter -        chr1:15477193              9.7                 58030           5990.8
20:42:35.823 INFO  ProgressMeter -        chr1:15642700              9.9                 58660           5945.1
20:42:48.790 INFO  ProgressMeter -        chr1:15837013             10.1                 59430           5894.0
20:42:59.781 INFO  ProgressMeter -        chr1:15934169             10.3                 59800           5824.9
20:43:09.899 INFO  ProgressMeter -        chr1:16031936             10.4                 60180           5767.2
20:43:19.923 INFO  ProgressMeter -        chr1:16118619             10.6                 60530           5709.3
20:43:30.350 INFO  ProgressMeter -        chr1:16368181             10.8                 61500           5707.3
20:43:40.690 INFO  ProgressMeter -        chr1:16487729             10.9                 61950           5658.5
20:43:51.053 INFO  ProgressMeter -        chr1:16599954             11.1                 62370           5608.4
20:44:01.103 INFO  ProgressMeter -        chr1:16664577             11.3                 62630           5548.2
20:44:11.453 INFO  ProgressMeter -        chr1:16831166             11.5                 63250           5518.8
20:44:21.456 INFO  ProgressMeter -        chr1:16899986             11.6                 63500           5461.2
20:44:32.207 INFO  ProgressMeter -        chr1:17003592             11.8                 63920           5413.9
20:44:42.246 INFO  ProgressMeter -        chr1:17280679             12.0                 64960           5425.1
20:44:45.240 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.09514966700000001
20:44:45.240 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 25.144886835
20:44:45.240 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 44.67 sec
20:44:45.241 INFO  Mutect2 - Shutting down engine
[December 5, 2023 8:44:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 12.09 minutes.
Runtime.totalMemory()=1038024704
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:659)
    at java.util.ArrayList.get(ArrayList.java:435)
    at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.lambda$getGermlineAltAlleleFrequencies$27(SomaticGenotypingEngine.java:351)
    at java.util.stream.ReferencePipeline$6$1.accept(ReferencePipeline.java:244)
    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:546)
    at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
    at java.util.stream.DoublePipeline.toArray(DoublePipeline.java:530)
    at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.getGermlineAltAlleleFrequencies(SomaticGenotypingEngine.java:353)
    at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.getNegativeLogPopulationAFAnnotation(SomaticGenotypingEngine.java:336)
    at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:155)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:259)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:299)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    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)