Hi, anyone has encountered this before?

I encountered this error when following the somatic CNV guideline on my WGS paired normal-tumor samples. No output except hets.tsv & hets.normal.tsv. Any help appreciated. thank you!

The CollectAllelicCount was ran on 1000g_hg38snphigh confidence.vcf.gz (generated using SelectVariant using AF > 0.1. (i can't find the gnomad wgs on resource bundle). 

a) GATK version used: v4.2.5.0
b) Exact command used: 

$GATK ModelSegments --denoised-copy-ratios T${SAMPLE}.denoisedCR.tsv --allelic-counts AlleleCount/T${SAMPLE}.allelicCounts.tsv --normal-allelic-counts AlleleCount/N${SAMPLE}.allelicCounts.tsv --output . --output-prefix ${SAMPLE}.cr

c) Entire program log:

09:52:54.356 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/csittz/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 19, 2022 9:52:55 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
09:52:55.525 INFO  ModelSegments - ------------------------------------------------------------
09:52:55.526 INFO  ModelSegments - The Genome Analysis Toolkit (GATK) v4.2.5.0
09:52:55.526 INFO  ModelSegments - For support and documentation go to https://software.broadinstitute.org/gatk/
09:52:55.527 INFO  ModelSegments - Executing as csittz@CSI-BTX7ZH3 on Linux v4.4.0-19041-Microsoft amd64
09:52:55.530 INFO  ModelSegments - Java runtime: OpenJDK 64-Bit Server VM v11.0.11+9-Ubuntu-0ubuntu2.20.04
09:52:55.530 INFO  ModelSegments - Start Date/Time: April 19, 2022 at 9:52:54 AM SGT
09:52:55.531 INFO  ModelSegments - ------------------------------------------------------------
09:52:55.531 INFO  ModelSegments - ------------------------------------------------------------
09:52:55.533 INFO  ModelSegments - HTSJDK Version: 2.24.1
09:52:55.533 INFO  ModelSegments - Picard Version: 2.25.4
09:52:55.534 INFO  ModelSegments - Built for Spark Version: 2.4.5
09:52:55.534 INFO  ModelSegments - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:52:55.535 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:52:55.535 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:52:55.535 INFO  ModelSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:52:55.536 INFO  ModelSegments - Deflater: IntelDeflater
09:52:55.536 INFO  ModelSegments - Inflater: IntelInflater
09:52:55.537 INFO  ModelSegments - GCS max retries/reopens: 20
09:52:55.537 INFO  ModelSegments - Requester pays: disabled
09:52:55.538 INFO  ModelSegments - Initializing engine
09:52:55.539 INFO  ModelSegments - Done initializing engine
09:52:55.539 INFO  ModelSegments - Used memory (MB) after initializing engine: 34
09:52:55.547 INFO  ModelSegments - Reading file (T02.denoisedCR.tsv)...
09:52:55.625 INFO  ModelSegments - Reading file (AlleleCount/T02.allelicCounts.tsv)...
09:53:01.086 INFO  ModelSegments - Reading file (AlleleCount/N02.allelicCounts.tsv)...
09:53:05.855 INFO  ModelSegments - Used memory (MB) after reading files: 1756
09:53:06.749 INFO  ModelSegments - Used memory (MB) after validating data: 1703
09:53:07.495 INFO  NaiveHeterozygousPileupGenotypingUtils - Genotyping heterozygous sites from available allelic counts...
09:53:07.496 INFO  NaiveHeterozygousPileupGenotypingUtils - Matched normal was provided, running in matched-normal mode...
09:53:08.381 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 3855068 / 5090504 sites after filtering allelic counts with total count less than 30 in matched-normal sample N02...
09:53:09.223 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 3855042 / 5090504 sites after filtering on overlap with copy-ratio intervals in matched-normal sample N02...
09:53:15.402 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 1118178 / 5090504 sites after filtering on heterozygosity in matched-normal sample N02...
09:53:15.403 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 5090504 / 5090504 sites after filtering allelic counts with total count less than 0 in case sample T02...
09:53:16.509 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 5089851 / 5090504 sites after filtering on overlap with copy-ratio intervals in case sample T02...
09:53:16.510 INFO  NaiveHeterozygousPileupGenotypingUtils - Retaining allelic counts for case sample N02 at heterozygous sites in matched-normal sample T02...
09:53:17.761 INFO  NaiveHeterozygousPileupGenotypingUtils - Retained 1118178 / 5090504 sites after applying all filters to case sample T02.
09:53:18.003 INFO  ModelSegments - Used memory (MB) after genotyping: 3080
09:53:18.004 INFO  ModelSegments - Writing heterozygous allelic counts for matched normal to /mnt/d/LR_Lung/CNV/./02.cr.hets.normal.tsv...
09:53:18.811 INFO  ModelSegments - Writing allelic counts for case sample at heterozygous sites in matched normal to /mnt/d/LR_Lung/CNV/./02.cr.hets.tsv...
09:53:20.772 INFO  MultisampleMultidimensionalKernelSegmenter - Using first allelic-count site in each copy-ratio interval (114 / 1118178) for multidimensional segmentation...
09:53:20.786 INFO  MultisampleMultidimensionalKernelSegmenter - Finding changepoints in (333, 1118178) data points and 24 chromosomes across 1 sample(s)...
09:53:20.787 INFO  MultisampleMultidimensionalKernelSegmenter - Finding changepoints in 15 data points in chromosome chr1...
09:53:20.789 WARN  KernelSegmenter - Specified dimension of the kernel approximation (100) exceeds the number of data points (15) to segment; using all data points to calculate kernel matrix.
09:53:20.808 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 16) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.809 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 32) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.810 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 64) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.811 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 128) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.811 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 256) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.812 WARN  KernelSegmenter - Number of points needed to calculate local changepoint costs (2 * window size = 512) exceeds number of data points (15).  Local changepoint costs will not be calculated for this window size.
09:53:20.812 WARN  KernelSegmenter - No changepoint candidates were found.  The specified window sizes may be inappropriate, or there may be insufficient data points.

.....

09:53:20.997 INFO  GibbsSampler - Starting MCMC sampling.
09:53:21.057 INFO  GibbsSampler - 25 of 100 samples generated.
09:53:21.095 INFO  GibbsSampler - 50 of 100 samples generated.
09:53:21.126 INFO  GibbsSampler - 75 of 100 samples generated.
09:53:21.149 INFO  GibbsSampler - 100 of 100 samples generated.
09:53:21.149 INFO  GibbsSampler - MCMC sampling complete.
09:53:21.150 INFO  MultidimensionalModeller - Fitting allele-fraction model...
09:53:21.155 INFO  ModelSegments - Shutting down engine
[April 19, 2022 at 9:53:21 AM SGT] org.broadinstitute.hellbender.tools.copynumber.ModelSegments done. Elapsed time: 0.45 minutes.
Runtime.totalMemory()=14323548160
java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match.
        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
        at org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionModeller.<init>(AlleleFractionModeller.java:83)
        at org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller.fitModel(MultidimensionalModeller.java:107)
        at org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller.<init>(MultidimensionalModeller.java:90)
        at org.broadinstitute.hellbender.tools.copynumber.ModelSegments.doWork(ModelSegments.java:571)
        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)