Hi, I am running the pipeline and I get this error:

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (SRR1598405)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (SRR1598405)` terminated with an error exit status (1)


Command executed:

  picard \
      RenameSampleInVcf \
      -Xmx4915M \
      --INPUT SRR1598405_repeat_expansion.vcf \
      --OUTPUT SRR1598405_renam.vcf.gz \
       --NEW_SAMPLE_NAME SRR1598405
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP":
      picard: $(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
  14:14:45.850 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.3.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
  [Tue Oct 14 14:14:45 GMT 2025] RenameSampleInVcf --INPUT SRR1598405_repeat_expansion.vcf --OUTPUT SRR1598405_renam.vcf.gz --NEW_SAMPLE_NAME SRR1598405 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Tue Oct 14 14:14:46 GMT 2025] Executing as karla.ruiz@cnode33 on Linux 4.18.0-477.13.1.el8_8.x86_64 amd64; OpenJDK 64-Bit Server VM 22.0.1-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
  [Tue Oct 14 14:14:46 GMT 2025] picard.vcf.RenameSampleInVcf done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=2075918336
  To get help, see <http://broadinstitute.github.io/picard/index.html#GettingHelp>
  Exception in thread "main" java.lang.IllegalStateException: Key REF found in VariantContext field INFO at chr1:57367043 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
  	at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:215)
  	at htsjdk.variant.vcf.VCFEncoder.write(VCFEncoder.java:148)
  	at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:250)
  	at picard.vcf.RenameSampleInVcf.doWork(RenameSampleInVcf.java:134)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
  	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
  	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)

I use the variant catalog provided here: https://github.com/Clinical-Genomics/reference-files/blob/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/variant_catalog_grch38.json At this point I'm skipping this step but it would be nice to have some feedback about this.

I also had some error with CALL_REPEAT_EXPANSIONS not exactly this one but a different one, so I skipped it too for now.

Hi Karla! Can you run the pipeline with this file and see if the error persists? https://github.com/Clinical-Genomics/stranger/blob/main/stranger/resources/variant_catalog_grch38.json