I am running into imcompatible contigs error. I checked the reference fasta and the dict file with the interval file. The contigs are the same, they match (they both dont have "chr" in front of the chromosome names) and they are in the right order. Infact, I concatenated the dict file and the bed file together to create the interval file and the file's name has .interval_list extension as recognized by the too. But I still get this error. Can someone kindly help. 

REQUIRED for all errors and issues:
a) GATK version used: 4.1.9.0

b) Exact command used:

singularity exec
-e --no-home broadinstitute-gatk-4.1.9.0.img
gatk CollectReadCounts
-L /Agilent_V4_mergebed_preprocessed.interval_list
-R human_g1k_v37_decoy.fasta
--interval-merging-rule OVERLAPPING_ONLY
--output AGI_ploidy
--verbosity DEBUG
-I Sample1.hdf5

c) Entire program log:

00:16:13.127 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.9.0-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
00:16:13.210 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression6756995224704301046.so
May 04, 2024 12:16:13 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
00:16:13.365 INFO  CollectReadCounts - ------------------------------------------------------------
00:16:13.366 INFO  CollectReadCounts - The Genome Analysis Toolkit (GATK) v4.1.9.0-SNAPSHOT
00:16:13.366 INFO  CollectReadCounts - For support and documentation go to https://software.broadinstitute.org/gatk/
00:16:13.366 INFO  CollectReadCounts - Executing as ravichav@terra on Linux v3.10.0-1160.45.1.el7.x86_64 amd64
00:16:13.366 INFO  CollectReadCounts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
00:16:13.366 INFO  CollectReadCounts - Start Date/Time: May 4, 2024 12:16:13 AM GMT
00:16:13.366 INFO  CollectReadCounts - ------------------------------------------------------------
00:16:13.366 INFO  CollectReadCounts - ------------------------------------------------------------
00:16:13.367 INFO  CollectReadCounts - HTSJDK Version: 2.23.0
00:16:13.367 INFO  CollectReadCounts - Picard Version: 2.23.3
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.BUFFER_SIZE : 131072
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.CREATE_INDEX : false
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.CREATE_MD5 : false
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.CUSTOM_READER_FACTORY : 
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
00:16:13.368 INFO  CollectReadCounts - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.REFERENCE_FASTA : null
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:16:13.369 INFO  CollectReadCounts - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
00:16:13.369 DEBUG ConfigFactory - Configuration file values: 
00:16:13.372 DEBUG ConfigFactory -     gcsMaxRetries = 20
00:16:13.372 DEBUG ConfigFactory -     gcsProjectForRequesterPays = 
00:16:13.372 DEBUG ConfigFactory -     gatk_stacktrace_on_user_exception = false
00:16:13.372 DEBUG ConfigFactory -     samjdk.use_async_io_read_samtools = false
00:16:13.372 DEBUG ConfigFactory -     samjdk.use_async_io_write_samtools = true
00:16:13.372 DEBUG ConfigFactory -     samjdk.use_async_io_write_tribble = false
00:16:13.372 DEBUG ConfigFactory -     samjdk.compression_level = 2
00:16:13.372 DEBUG ConfigFactory -     spark.kryoserializer.buffer.max = 512m
00:16:13.372 DEBUG ConfigFactory -     spark.driver.maxResultSize = 0
00:16:13.372 DEBUG ConfigFactory -     spark.driver.userClassPathFirst = true
00:16:13.372 DEBUG ConfigFactory -     spark.io.compression.codec = lzf
00:16:13.372 DEBUG ConfigFactory -     spark.executor.memoryOverhead = 600
00:16:13.372 DEBUG ConfigFactory -     spark.driver.extraJavaOptions = 
00:16:13.372 DEBUG ConfigFactory -     spark.executor.extraJavaOptions = 
00:16:13.373 DEBUG ConfigFactory -     codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
00:16:13.373 DEBUG ConfigFactory -     read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
00:16:13.376 DEBUG ConfigFactory -     annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
00:16:13.376 DEBUG ConfigFactory -     cloudPrefetchBuffer = 40
00:16:13.376 DEBUG ConfigFactory -     cloudIndexPrefetchBuffer = -1
00:16:13.376 DEBUG ConfigFactory -     createOutputBamIndex = true
00:16:13.376 INFO  CollectReadCounts - Deflater: IntelDeflater
00:16:13.376 INFO  CollectReadCounts - Inflater: IntelInflater
00:16:13.376 INFO  CollectReadCounts - GCS max retries/reopens: 20
00:16:13.376 INFO  CollectReadCounts - Requester pays: disabled
00:16:13.376 INFO  CollectReadCounts - Initializing engine
DEBUG    2024-05-04 00:16:13    Option    Ignoring CACHE_FILE_BASED_INDEXES option; does not apply to PrimitiveSamReaderToSamReaderAdapter readers.
00:16:13.683 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
00:16:13.683 DEBUG GenomeLocParser -  1 (249250621 bp)
00:16:13.683 DEBUG GenomeLocParser -  2 (243199373 bp)
00:16:13.683 DEBUG GenomeLocParser -  3 (198022430 bp)
00:16:13.683 DEBUG GenomeLocParser -  4 (191154276 bp)
00:16:13.683 DEBUG GenomeLocParser -  5 (180915260 bp)
00:16:13.683 DEBUG GenomeLocParser -  6 (171115067 bp)
00:16:13.683 DEBUG GenomeLocParser -  7 (159138663 bp)
00:16:13.684 DEBUG GenomeLocParser -  8 (146364022 bp)
00:16:13.684 DEBUG GenomeLocParser -  9 (141213431 bp)
00:16:13.684 DEBUG GenomeLocParser -  10 (135534747 bp)
00:16:13.684 DEBUG GenomeLocParser -  11 (135006516 bp)
00:16:13.684 DEBUG GenomeLocParser -  12 (133851895 bp)
00:16:13.684 DEBUG GenomeLocParser -  13 (115169878 bp)
00:16:13.684 DEBUG GenomeLocParser -  14 (107349540 bp)
00:16:13.685 DEBUG GenomeLocParser -  15 (102531392 bp)
00:16:13.685 DEBUG GenomeLocParser -  16 (90354753 bp)
00:16:13.685 DEBUG GenomeLocParser -  17 (81195210 bp)
00:16:13.685 DEBUG GenomeLocParser -  18 (78077248 bp)
00:16:13.685 DEBUG GenomeLocParser -  19 (59128983 bp)
00:16:13.685 DEBUG GenomeLocParser -  20 (63025520 bp)
00:16:13.685 DEBUG GenomeLocParser -  21 (48129895 bp)
00:16:13.685 DEBUG GenomeLocParser -  22 (51304566 bp)
00:16:13.686 DEBUG GenomeLocParser -  X (155270560 bp)
00:16:13.686 DEBUG GenomeLocParser -  Y (59373566 bp)
00:16:13.686 DEBUG GenomeLocParser -  MT (16569 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000207.1 (4262 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000226.1 (15008 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000229.1 (19913 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000231.1 (27386 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000210.1 (27682 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000239.1 (33824 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000235.1 (34474 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000201.1 (36148 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000247.1 (36422 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000245.1 (36651 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000197.1 (37175 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000203.1 (37498 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000246.1 (38154 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000249.1 (38502 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000196.1 (38914 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000248.1 (39786 bp)
00:16:13.686 DEBUG GenomeLocParser -  GL000244.1 (39929 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000238.1 (39939 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000202.1 (40103 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000234.1 (40531 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000232.1 (40652 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000206.1 (41001 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000240.1 (41933 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000236.1 (41934 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000241.1 (42152 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000243.1 (43341 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000242.1 (43523 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000230.1 (43691 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000237.1 (45867 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000233.1 (45941 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000204.1 (81310 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000198.1 (90085 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000208.1 (92689 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000191.1 (106433 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000227.1 (128374 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000228.1 (129120 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000214.1 (137718 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000221.1 (155397 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000209.1 (159169 bp)
00:16:13.687 DEBUG GenomeLocParser -  GL000218.1 (161147 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000220.1 (161802 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000213.1 (164239 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000211.1 (166566 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000199.1 (169874 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000217.1 (172149 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000216.1 (172294 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000215.1 (172545 bp)
00:16:13.688 DEBUG GenomeLocParser -  GL000205.1 (174588 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000219.1 (179198 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000224.1 (179693 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000223.1 (180455 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000195.1 (182896 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000212.1 (186858 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000222.1 (186861 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000200.1 (187035 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000193.1 (189789 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000194.1 (191469 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000225.1 (211173 bp)
00:16:13.689 DEBUG GenomeLocParser -  GL000192.1 (547496 bp)
00:16:13.689 DEBUG GenomeLocParser -  NC_007605 (171823 bp)
00:16:13.690 DEBUG GenomeLocParser -  hs37d5 (35477943 bp)
00:16:13.709 INFO  FeatureManager - Using codec IntervalListCodec to read file file://Agilent_V4_mergebed_preprocessed.interval_list
00:16:14.474 DEBUG FeatureDataSource - Cache statistics for FeatureInput Agilent_V4_mergebed_preprocessed.interval_list:Agilent_V4_mergebed_preprocessed.interval_list:
00:16:14.475 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
00:16:14.551 INFO  IntervalArgumentCollection - Processing 51189318 bp from intervals
00:16:14.587 INFO  CollectReadCounts - Shutting down engine
[May 4, 2024 12:16:14 AM GMT] org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2501902336
***********************************************************************

A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
  reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605, hs37d5]
  reads contigs = []

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.1.9.0-SNAPSHOT-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 /gatk/gatk-package-4.1.9.0-SNAPSHOT-local.jar CollectReadCounts -L Agilent_V4_mergebed_preprocessed.interval_list -R human_g1k_v37_decoy.fasta --interval-merging-rule OVERLAPPING_ONLY --output AGI_ploidy --verbosity DEBUG -I Sample1.hdf5