I am trying to call mouse variants for grcm39 using gatk and running into the error described below. I've search the snp file and the interval queried does not exist in the file?

Thanks so much for all your assistance.

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

The Genome Analysis Toolkit (GATK) v4.1.8.1

b) Exact command used:

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 -Xms4G -jar /gatk/gatk-package-4.1.8.1-local.jar BaseRecalibrator -R /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/Mus_musculus.GRCm39.dna.primary_assembly.fa -I /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/submissions/66a0b5bf-1e94-4e51-bdaf-886055953977/PreProcessingForVariantDiscovery_GATK4/baa27599-1fdf-4500-9238-2f0b8dcfe023/call-SortAndFixTags/cacheCopy/20191210_AN4_BH7589_S4.grcm39.aligned.duplicate_marked.sorted.bam --use-original-qualities -O 20191210_AN4_BH7589_S4.grcm39.recal_data.csv --known-sites /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_snps.rsID.vcf.gz --known-sites /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_indels.rsID.vcf.gz -L 1:1+

c) Entire program log:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.WSPzki
13:31:32.850 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:31:34.721 INFO  BaseRecalibrator - ------------------------------------------------------------
13:31:34.721 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.8.1
13:31:34.721 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:31:34.722 INFO  BaseRecalibrator - Executing as root@36446dd73f8a on Linux v6.1.75+ amd64
13:31:34.723 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
13:31:34.723 INFO  BaseRecalibrator - Start Date/Time: May 14, 2024 1:31:32 PM GMT
13:31:34.723 INFO  BaseRecalibrator - ------------------------------------------------------------
13:31:34.724 INFO  BaseRecalibrator - ------------------------------------------------------------
13:31:34.726 INFO  BaseRecalibrator - HTSJDK Version: 2.23.0
13:31:34.726 INFO  BaseRecalibrator - Picard Version: 2.22.8
13:31:34.727 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:31:34.727 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:31:34.727 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:31:34.728 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:31:34.728 INFO  BaseRecalibrator - Deflater: IntelDeflater
13:31:34.733 INFO  BaseRecalibrator - Inflater: IntelInflater
13:31:34.734 INFO  BaseRecalibrator - GCS max retries/reopens: 20
13:31:34.734 INFO  BaseRecalibrator - Requester pays: disabled
13:31:34.734 INFO  BaseRecalibrator - Initializing engine
WARNING: BAM index file /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/submissions/66a0b5bf-1e94-4e51-bdaf-886055953977/PreProcessingForVariantDiscovery_GATK4/baa27599-1fdf-4500-9238-2f0b8dcfe023/call-SortAndFixTags/cacheCopy/20191210_AN4_BH7589_S4.grcm39.aligned.duplicate_marked.sorted.bai is older than BAM /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/submissions/66a0b5bf-1e94-4e51-bdaf-886055953977/PreProcessingForVariantDiscovery_GATK4/baa27599-1fdf-4500-9238-2f0b8dcfe023/call-SortAndFixTags/cacheCopy/20191210_AN4_BH7589_S4.grcm39.aligned.duplicate_marked.sorted.bam
13:31:35.557 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_snps.rsID.vcf.gz
13:31:35.790 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_indels.rsID.vcf.gz
13:31:36.062 INFO  IntervalArgumentCollection - Processing 195154279 bp from intervals
13:31:36.081 INFO  BaseRecalibrator - Done initializing engine
13:31:36.083 WARN  BaseRecalibrator - This tool has only been well tested on ILLUMINA-based sequencing data. For other data use at your own risk.
13:31:36.131 INFO  BaseRecalibrationEngine - The covariates being used here: 
13:31:36.132 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
13:31:36.132 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
13:31:36.132 INFO  BaseRecalibrationEngine - 	ContextCovariate
13:31:36.133 INFO  BaseRecalibrationEngine - 	CycleCovariate
13:31:36.145 INFO  ProgressMeter - Starting traversal
13:31:36.146 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
13:31:46.177 INFO  ProgressMeter -           1:21583071              0.2                 45000         269649.5
13:31:48.143 INFO  BaseRecalibrator - Shutting down engine
[May 14, 2024 1:31:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=4151836672
org.broadinstitute.hellbender.exceptions.GATKException: Error querying file /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_snps.rsID.vcf.gz over interval 1:29605331-29605354
	at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:570)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536)
	at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352)
	at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
	at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
	at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:263)
	at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:185)
	at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
	at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:94)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.io.IOException: Invalid argument
	at java.io.RandomAccessFile.seek0(Native Method)
	at java.io.RandomAccessFile.seek(RandomAccessFile.java:557)
	at htsjdk.samtools.seekablestream.SeekableFileStream.seek(SeekableFileStream.java:63)
	at htsjdk.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.<init>(TribbleIndexedFeatureReader.java:579)
	at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.advanceBlock(TribbleIndexedFeatureReader.java:470)
	at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.<init>(TribbleIndexedFeatureReader.java:440)
	at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:297)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:567)
	... 27 more
Using GATK jar /gatk/gatk-package-4.1.8.1-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 -Xms4G -jar /gatk/gatk-package-4.1.8.1-local.jar BaseRecalibrator -R /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/Mus_musculus.GRCm39.dna.primary_assembly.fa -I /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/submissions/66a0b5bf-1e94-4e51-bdaf-886055953977/PreProcessingForVariantDiscovery_GATK4/baa27599-1fdf-4500-9238-2f0b8dcfe023/call-SortAndFixTags/cacheCopy/20191210_AN4_BH7589_S4.grcm39.aligned.duplicate_marked.sorted.bam --use-original-qualities -O 20191210_AN4_BH7589_S4.grcm39.recal_data.csv --known-sites /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_snps.rsID.vcf.gz --known-sites /cromwell_root/fc-7711ee16-4d3a-44ca-b176-8acc97dff57a/ref/GRCm39/mgp_REL2021_indels.rsID.vcf.gz -L 1:1+