ERROR: genmod.commands.score_variants

[karlaarz]

Description of the bug

Hello!

I am running the pipeline and get this error with Genmod SV file. I am using the rank model files from here

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (test1)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (test1)` terminated with an error exit status (1)


Command executed:

  genmod \
      score \
      --rank_results \
      --family_file test1.ped \
      --score_config rank_model_sv.ini \
      --outfile test1_sv_genmod_score_research_score.vcf \
      test1_sv_genmod_models_research_models.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE":
      genmod: $(echo $(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  [2025-10-28 10:32:58,890] WARNING : genmod.score_variants.check_plugins: INFO field GeneticModels is not in vcf INFO. This field will not be scored.
  [2025-10-28 10:32:58,890] WARNING : genmod.score_variants.check_plugins: INFO field ModelScore is not in vcf INFO. This field will not be scored.
  [2025-10-28 10:32:58,890] ERROR   : genmod.commands.score_variants: All score plugins has to be defined in vcf header
  Aborted!

Command used and terminal output

nextflow run raredisease/main.nf \
    -profile ht_cluster \
    -params-file scripts/params.yaml -c scripts/custom.config \
    -resume

Relevant files

params.yaml

the custom.config file:

process {
    executor = 'slurm'
    
    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD' {
        memory = '32.GB'
        cpus = 2
        time = '6.h'
    }
    
    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIS' {
        memory = '32.GB'
        cpus = 2
        time = '4.h'
    }
    
    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT' {
        memory = '32.GB'
        cpus = 2
        time = '4.h'
    }
    
    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION' {
        memory = '32.GB'
        cpus = 2
        time = '4.h'
    }
    
    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL' {
        memory = '32.GB'
        cpus = 2
        time = '4.h'
    }
}

System information

Nextflow version - 24.04.4

[jemten]

Hello @karlaarz,
Could you send a small excerpt of the vcf used as input for that process?