Hi, I am running nf-core-rd version 2.3.0 (in offline mode) and am getting a genmod error as listed below. The used genmod version is 3.9. The error only occures when running a trio (giab-ashkenazi), not single sample (HG002). According to https://github.com/Clinical-Genomics/genmod/issues/171 a similar problem, that has to do with the used sort command, occurs for version 10 of genmod (but not for 3.9). Any ideas how I could get around this?

Apr-16 20:43:58.870 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (giab_askenashi)'

Caused by:
  Process exceeded running time limit (8h)


Command executed:

  genmod \
      compound \
      --temp_dir ./ \
      --processes 6 \
      --outfile giab_askenashi_mt_genmod_compound_research_compound.vcf \
      giab_askenashi_mt_genmod_score_research_score.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND":
      genmod: $(echo $(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Command error:
  Process CompoundScorer-2:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
      self.run()
    File "/usr/local/lib/python3.8/site-packages/genmod/score_variants/compound_scorer.py", line 239, in run
      compound_rank_score = rank_scores[rank_score_type][compound_id]
  <https://dsp.aida.scilifelab.se/ctaccess?lid=464aa720-480b-4917-9038-4575aa764c88>


  Process CompoundScorer-4:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
      self.run()
    File "/usr/local/lib/python3.8/site-packages/genmod/score_variants/compound_scorer.py", line 239, in run
      compound_rank_score = rank_scores[rank_score_type][compound_id]
  KeyError: 'MT_3318_C_CTATAATT'
  Process CompoundScorer-5:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
      self.run()
    File "/usr/local/lib/python3.8/site-packages/genmod/score_variants/compound_scorer.py", line 239, in run
      compound_rank_score = rank_scores[rank_score_type][compound_id]
  KeyError: 'MT_2361_GA_CC'
  Process CompoundScorer-3:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
      self.run()
    File "/usr/local/lib/python3.8/site-packages/genmod/score_variants/compound_scorer.py", line 239, in run
      compound_rank_score = rank_scores[rank_score_type][compound_id]
  KeyError: 'MT_13687_C_T'
  Process CompoundScorer-7:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
      self.run()
    File "/usr/local/lib/python3.8/site-packages/genmod/score_variants/compound_scorer.py", line 239, in run
      compound_rank_score = rank_scores[rank_score_type][compound_id]
  KeyError: 'MT_15229_T_G'

Hi Halfdan, if this error also stems from the sorting you could try running genmod with one cpu as a workaround. If the MT variants input to genmod are sorted it might work.

Thank you Felix, I got lost in other things with running the pipeline, but will get back if I see that this worked.