I'm using gatk 4.2.5.0 and trying to use the hg38 PoN_4.0_WGS_for_public.pon.hdf5 to normalize CNV calls for some WGS samples I have.  I keep getting an error saying the sample intervals must patch the original intervals used to build the panel of normals.  Since I didn't build this panel, I don't know what these original intervals are and haven't been able to find good documentation of this. 

These are the commands I've tried:

1. Create intervals with 1000bp bins using gatk publicly available files (wgs_coverage_regions.hg38.interval_list)

 ~/bin/gatk-4.2.5.0/gatk PreprocessIntervals -L ../reference_files/hg38/wgs_coverage_regions.hg38.interval_list -R ../reference_files/hg38/Homo_sapiens_assembly38.fasta --bin-length 1000 --interval-merging-rule OVERLAPPING_ONLY -O wgs_coverage_regions.hg38.1k.preprocessed.interval_list

1. get read counts over intervals for my sample

 ~/bin/gatk-4.2.5.0/gatk CollectReadCounts -I bam/SL497849.hg38.bam -L wgs_coverage_regions.hg38.1k.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY -O frag_counts_wgscov2/SL497849.counts.hdf5

2. Try to use the public PoN to denoise the counts

~/bin/gatk-4.2.5.0/gatk --java-options "-Xmx12g" DenoiseReadCounts -I frag_counts_wgscov2/SL497849.counts.hdf5 --count-panel-of-normals ~/reference_files/hg38/PoN_4.0_WGS_for_public.pon.hdf5 --standardized-copy-ratios cnv_results/SL497846.standardizedCR.tsv --denoised-copy-ratios cnv_results/SL497846.denoisedCR.tsv 

This is the error log I get at the last step:

Using GATK jar /home/ballint2/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -Xmx12g -jar /home/ballint2/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar DenoiseReadCounts -I frag_counts_wgscov2/SL497849.counts.hdf5 --count-panel-of-normals /home/ballint2/reference_files/hg38/PoN_4.0_WGS_for_public.pon.hdf5 --standardized-copy-ratios cnv_results/SL497846.standardizedCR.tsv --denoised-copy-ratios cnv_results/SL497846.denoisedCR.tsv
12:23:52.839 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/ballint2/bin/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 14, 2022 12:23:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:23:53.376 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:53.376 INFO  DenoiseReadCounts - The Genome Analysis Toolkit (GATK) v4.2.5.0
12:23:53.376 INFO  DenoiseReadCounts - For support and documentation go to https://software.broadinstitute.org/gatk/
12:23:53.376 INFO  DenoiseReadCounts - Executing as ballint2@ip-172-25-130-233.rdcloud.bms.com on Linux v4.18.0-365.el8.x86_64 amd64
12:23:53.376 INFO  DenoiseReadCounts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_322-b06
12:23:53.377 INFO  DenoiseReadCounts - Start Date/Time: March 14, 2022 12:23:52 PM EDT
12:23:53.377 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:53.377 INFO  DenoiseReadCounts - ------------------------------------------------------------
12:23:53.377 INFO  DenoiseReadCounts - HTSJDK Version: 2.24.1
12:23:53.378 INFO  DenoiseReadCounts - Picard Version: 2.25.4
12:23:53.378 INFO  DenoiseReadCounts - Built for Spark Version: 2.4.5
12:23:53.378 INFO  DenoiseReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:23:53.378 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:23:53.378 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:23:53.378 INFO  DenoiseReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:23:53.378 INFO  DenoiseReadCounts - Deflater: IntelDeflater
12:23:53.378 INFO  DenoiseReadCounts - Inflater: IntelInflater
12:23:53.378 INFO  DenoiseReadCounts - GCS max retries/reopens: 20
12:23:53.378 INFO  DenoiseReadCounts - Requester pays: disabled
12:23:53.379 INFO  DenoiseReadCounts - Initializing engine
12:23:53.379 INFO  DenoiseReadCounts - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
12:23:53.529 INFO  DenoiseReadCounts - Reading read-counts file (frag_counts_wgscov2/SL497849.counts.hdf5)...
12:23:55.676 INFO  SVDDenoisingUtils - Validating sample intervals against original intervals used to build panel of normals...
12:23:59.360 INFO  DenoiseReadCounts - Shutting down engine
[March 14, 2022 12:23:59 PM EDT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=2469920768
java.lang.IllegalArgumentException: Sample intervals must be identical to the original intervals used to build the panel of normals.
        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils.denoise(SVDDenoisingUtils.java:119)
        at org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals.denoise(SVDReadCountPanelOfNormals.java:88)
        at org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.doWork(DenoiseReadCounts.java:204)
        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)

Thank you for any help.