I’m trying to run the test-profile of raredisease v2.2.0, but get:

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky)` terminated with an error exit status (255)


Command executed:

  vep \
      -i justhusky_view.vcf \
      -o justhusky_svdbquery_vep.vcf.gz \
      --dir_cache vep_cache --dir_plugins vep_cache/Plugins --plugin pLI,pLI_values.txt --appris --biotype --buffer_size 100 --canonical --cache --ccds --compress_output bgzip --distance 5000 --domains --exclude_predicted --force_overwrite --format vcf --fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged --no_progress --numbers --per_gene --polyphen p --protein --offline --regulatory --sift p --symbol --tsl --uniprot --vcf \
       \
      --fasta reference.fasta \
      --assembly GRCh37 \
      --species homo_sapiens \
      --cache \
      --cache_version 107 \
      --dir_cache ${PWD}/vep_cache \
      --fork 2
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV":
      ensemblvep: $( echo $(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  2024-12-10 22:54:56 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this

Command error:
  2024-12-10 22:54:56 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
  Can't locate object method "cdna_coords" via package "Bio::EnsEMBL::Variation::StructuralVariationOverlap" at /usr/local/share/ensembl-vep-112.0-0/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 673.
  Died in forked process 2172

I get the same error on 2.20 test profile. I think this is a known issue, there seems to be an issue with VEP 112. I think the recommended solution for now is to use VEP 110 instead. You have to set parameter vep_cache_version to 110 and specify the VEP cache. (when running your own samples, this may not work for the test)

I see. I guess I shouldn’t complain since I’m not helping implement nf-core/raredisease, but I think it would be nice for all users - especially newcomers to nf-core pipelines - that both the test-profile and the test_full-profile run out-of-the-box.

Very much agreed. I think the test should be easy, but the test_full may require some work

I was aware that there was some issue with test_full, and that it required some work