I've just installed GATK and am trying to do some basic variant calling. However when I try and run this line

gatk Mutect2 -R $REF -I "$BAM" -O "$DIR"/gatk/$PREFIX"_bwa_gatk_unfiltered.vcf"

I get the error below. Reading the output, it looks like this is the line that goes wrong, but I don't know what it means!

WARN  NativeLibraryLoader - Unable to find native library: native/libgkl_pairhmm_omp.dylib

Here's the full error message:

Using GATK jar /Users/michaelflower/opt/anaconda3/envs/gatk4/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-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 /Users/michaelflower/opt/anaconda3/envs/gatk4/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar Mutect2 -R /Users/michaelflower/refs/hg38/chr5.fa -I /Users/michaelflower/Documents/ACL/Research/Projects/Illumina amplicon sequencing/2021.03.23 MiSeq test/40-498314829_copy3_MSH3repeat/bwa/MSH3repeat_bwa.bam -O /Users/michaelflower/Documents/ACL/Research/Projects/Illumina amplicon sequencing/2021.03.23 MiSeq test/40-498314829_copy3_MSH3repeat/gatk/MSH3repeat_bwa_gatk_unfiltered.vcf
16:56:38.459 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/michaelflower/opt/anaconda3/envs/gatk4/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
Nov 16, 2021 4:56:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:56:38.695 INFO  Mutect2 - ------------------------------------------------------------
16:56:38.695 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.3.0
16:56:38.695 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
16:56:38.695 INFO  Mutect2 - Executing as michaelflower@Michaels-MacBook-Pro-2.local on Mac OS X v10.16 x86_64
16:56:38.695 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08
16:56:38.696 INFO  Mutect2 - Start Date/Time: 16 November 2021 16:56:38 GMT
16:56:38.696 INFO  Mutect2 - ------------------------------------------------------------
16:56:38.696 INFO  Mutect2 - ------------------------------------------------------------
16:56:38.696 INFO  Mutect2 - HTSJDK Version: 2.24.1
16:56:38.696 INFO  Mutect2 - Picard Version: 2.25.4
16:56:38.696 INFO  Mutect2 - Built for Spark Version: 2.4.5
16:56:38.697 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:56:38.697 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:56:38.697 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:56:38.697 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:56:38.697 INFO  Mutect2 - Deflater: IntelDeflater
16:56:38.697 INFO  Mutect2 - Inflater: IntelInflater
16:56:38.697 INFO  Mutect2 - GCS max retries/reopens: 20
16:56:38.697 INFO  Mutect2 - Requester pays: disabled
16:56:38.697 INFO  Mutect2 - Initializing engine
16:56:39.108 INFO  Mutect2 - Done initializing engine
16:56:39.135 INFO  NativeLibraryLoader - Loading libgkl_utils.dylib from jar:file:/Users/michaelflower/opt/anaconda3/envs/gatk4/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_utils.dylib
16:56:39.309 WARN  NativeLibraryLoader - Unable to find native library: native/libgkl_pairhmm_omp.dylib
16:56:39.309 INFO  PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
16:56:39.309 INFO  NativeLibraryLoader - Loading libgkl_pairhmm.dylib from jar:file:/Users/michaelflower/opt/anaconda3/envs/gatk4/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm.dylib
16:56:39.466 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
16:56:39.466 WARN  IntelPairHmm - Ignoring request for 4 threads; not using OpenMP implementation
16:56:39.466 INFO  PairHMM - Using the AVX-accelerated native PairHMM implementation
16:56:39.468 INFO  Mutect2 - Shutting down engine
[16 November 2021 16:56:39 GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=488112128
java.lang.IllegalArgumentException: samples cannot be empty
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.<init>(ReferenceConfidenceModel.java:119)
    at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel.<init>(SomaticReferenceConfidenceModel.java:37)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.<init>(Mutect2Engine.java:159)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.onTraversalStart(Mutect2.java:261)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1083)
    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)
(gatk4)