Can't to pick contextual reference for validation dataset.

[cahuparo]

-[nf-core/pathogensurveillance] Pipeline completed with errors-
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ASSIGN_CONTEXT_REFERENCES (smarcescens)'

Caused by:
  Process `PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ASSIGN_CONTEXT_REFERENCES (smarcescens)` terminated with an error exit status (1)


Command executed:

  assign_context_references.R smarcescens_comp.csv smarcescens.csv 0 0 0 smarcescens_context_refs.csv
  
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ASSIGN_CONTEXT_REFERENCES":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in data.frame(sample_id = rep(sample_ids, each = n_refs_contextual),  : 
    arguments imply differing number of rows: 0, 327, 654
  Execution halted

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/ps_pipeline_validation/scripts/pathogensurveillance/work/bf/97670c9de38f9ac408dedbc5f2c324

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Here is how the ref_data.csv looks like:

ref_group_ids,ref_path,ref_ncbi_accession,ref_primary_usage,ref_contextual_usage
S_marcescens_Db11,,GCA_000513215.1,exclusive,excluded

Here I am excluding this reference because it is already par of the sample sheet. For this run, I don't want the pipeline to download references, I want it to build a reference free core gene phylogeny.