I get this error:

ERROR ~ Error executing process > 'NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS (SLPD001)'

Caused by:
  Process `NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS (SLPD001)` terminated with an error exit status (2)


Command executed:

  gatk --java-options "-Xmx9830M -XX:-UsePerfData" \
      CollectReadCounts \
      --input P2233_137_S2_L001_R1_001.bam \
      --intervals genome.interval_list \
      --output SLPD001.hdf5 \
      --reference Homo_sapiens_assembly38.fasta \
      --tmp-dir . \
      --format HDF5 --imr OVERLAPPING_ONLY
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CREATEPANELREFS:CREATEPANELREFS:GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Using GATK jar /opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-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 -Xmx9830M -XX:-UsePerfData -jar /opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar CollectReadCounts --input P2233_137_S2_L001_R1_001.bam --intervals genome.interval_list --output SLPD001.hdf5 --reference Homo_sapiens_assembly38.fasta --tmp-dir . --format HDF5 --imr OVERLAPPING_ONLY
  09:28:39.258 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  09:28:39.669 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.674 INFO  CollectReadCounts - The Genome Analysis Toolkit (GATK) v4.6.2.0
  09:28:39.675 INFO  CollectReadCounts - For support and documentation go to <https://software.broadinstitute.org/gatk/>
  09:28:39.675 INFO  CollectReadCounts - Executing as peter@monod33.mbb.ki.se on Linux v4.18.0-553.53.1.el8_10.x86_64 amd64
  09:28:39.675 INFO  CollectReadCounts - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
  09:28:39.676 INFO  CollectReadCounts - Start Date/Time: December 2, 2025 at 9:28:39 AM GMT
  09:28:39.676 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.676 INFO  CollectReadCounts - ------------------------------------------------------------
  09:28:39.677 INFO  CollectReadCounts - HTSJDK Version: 4.2.0
  09:28:39.678 INFO  CollectReadCounts - Picard Version: 3.4.0
  09:28:39.678 INFO  CollectReadCounts - Built for Spark Version: 3.5.0
  09:28:39.680 INFO  CollectReadCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  09:28:39.680 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  09:28:39.681 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  09:28:39.681 INFO  CollectReadCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  09:28:39.681 INFO  CollectReadCounts - Deflater: IntelDeflater
  09:28:39.681 INFO  CollectReadCounts - Inflater: IntelInflater
  09:28:39.681 INFO  CollectReadCounts - GCS max retries/reopens: 20
  09:28:39.681 INFO  CollectReadCounts - Requester pays: disabled
  09:28:39.682 INFO  CollectReadCounts - Initializing engine
  09:28:40.325 INFO  FeatureManager - Using codec IntervalListCodec to read file <file://genome.interval>_list
  09:28:49.587 INFO  IntervalArgumentCollection - Processing 3043969085 bp from intervals
  09:28:49.710 INFO  CollectReadCounts - Done initializing engine
  09:28:49.718 WARN  CollectReadCounts - Sequence dictionary in BAM does not match the master sequence dictionary.
  09:28:49.720 INFO  CollectReadCounts - Collecting read counts...
  09:28:49.721 INFO  ProgressMeter - Starting traversal
  09:28:49.721 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
  09:28:49.844 INFO  CollectReadCounts - Shutting down engine
  [December 2, 2025 at 9:28:49 AM GMT] org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts done. Elapsed time: 0.18 minutes.
  Runtime.totalMemory()=2088763392
  ***********************************************************************
  
  A USER ERROR has occurred: Contig chr1_KI270706v1_random not present in reads sequence dictionary
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:
  /datf/sl/users/ivana/BTB/raredisease/work/ef/f478d93adf8dfe766525651d998d6e

Container:  /datf/sl/users/ivana/BTB/raredisease/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-ce-ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0-data.img

This happens even though I removed all alignments to 'chr1_KI270706v1_random' from my bam files.

given that the tools complains about this contig, I'd say it's somewhere