ASSIGN_CONTEXT_REFERENCES error

[cahuparo]

This is the validation dataset.

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pathogensurveillance] Pipeline completed with errors-
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ASSIGN_CONTEXT_REFERENCES (validation_serratia)'

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


Command executed:

  assign_context_references.R validation_serratia_comp.csv validation_serratia.csv 0 0 0 validation_serratia_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, 544, 1088
  Execution halted

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/ps_pipeline_validation/scripts/pathogensurveillance/work/10/dcd1fd07a66928293825df55cd7161

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

[cahuparo]

The nextflow command looks like:

nextflow run main.nf --sample_data sample_data_N547_true.csv --reference_data ref_data.csv --outdir serratia_v1 --bakta_db nxf_dev/db -profile mamba,slurm,cqls --temp_dir ./tmp --hpc_queue bpp --max_total_jobs 10 --n_ref_species 0 --n_ref_genera 0 --n_ref_closest 0 --n_ref_closest_named 0 --n_ref_context 0 --n_ref_strains 0 --max_total_cpus 64 --max_total_memory 500.GB -resume 7f31caf5-4edf-444a-9b30-df2dd59a0243