I was running the pipeline with multiple samples and recently got this error for this specific sample other samples run fine. Is it possible to skip haplogrep3 for a specific sample. Moreover would there be a patch for this specific error for some samples where the coverage is apparently very low?

Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (case_KiGS23)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (case_KiGS23)` terminated with an error exit status (1)


Command executed:

  haplogrep3 \
      classify \
      --tree phylotree-rsrs@17.1 \
      --in case_KiGS23_mitochondria_hmtnote_vcfanno.vcf.gz \
      --out case_KiGS23_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT":
      haplogrep3: $(echo $(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
  END_VERSIONS

Command exit status:
  1

Command output:
  
  Haplogrep 3 3.2.2
  (c) 2022-2024 Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer
  Error: For input string: "."

Command error:
  java.lang.NumberFormatException: For input string: "."
      at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
      at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
      at java.base/java.lang.Double.parseDouble(Double.java:944)
      at java.base/java.lang.Double.valueOf(Double.java:906)
      at importer.VcfImporter.load(VcfImporter.java:209)
      at genepi.haplogrep3.haplogrep.io.readers.impl.VcfInputFileReader.read(VcfInputFileReader.java:39)
      at genepi.haplogrep3.haplogrep.io.readers.InputFileReaderFactory.read(InputFileReaderFactory.java:33)
      at genepi.haplogrep3.tasks.ClassificationTask.run(ClassificationTask.java:90)
      at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:96)
      at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:22)
      at picocli.CommandLine.executeUserObject(CommandLine.java:1783)
      at picocli.CommandLine.access$900(CommandLine.java:145)
      at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2150)
      at picocli.CommandLine$RunLast.handle(CommandLine.java:2144)
      at picocli.CommandLine$RunLast.handle(CommandLine.java:2108)
      at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:1975)
      at picocli.CommandLine.execute(CommandLine.java:1904)
      at genepi.haplogrep3.App.main(App.java:131)
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`