Test+Docker profile fails: Can't locate object method "cdna_coords"

[Oliversinn]

Description of the bug

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:
  2024-09-13 21:02:40 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this

Command error:
  2024-09-13 21:02:40 - 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 2112

Work dir:
  /home/tecniscan/Data/work/08/6ec046f9e7bea0a665d4ba8b2ae23c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- 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

Command used and terminal output

nextflow run nf-core/raredisease -profile test,docker --outdir results

Relevant files

nextflow.log

System information

Nextflow version: 24.04.4 build 5917
Hardware: Desktop
Executor: local
Container engine: Docker
OS: Linux Mint 22
Version of nf-core/raredisease: v2.2.0-gfa61a65

[jemten]

Thanks for reporting @Oliversinn,
looks like an issue with annotating breakpoint variants in VEP, Ensembl/ensembl-vep#1694 (comment). Looks like it will be patched in the next release of VEP (113). For now the workaround seems to be to remove the --regulatory flag in the ENSEMBLVEP_SV process config. We will test that change and patch the pipeline.

[jemten]

Yes, you would have to remove the --regulatory flag from the ENSEMBLVEP_SV process in this file conf/modules/annotate_structural_variants.configconf/modules/annotate_structural_variants.config even when running with you data,

[Oliversinn]

Now I am getting the following:

-[nf-core/raredisease] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ (justhusky)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ (justhusky)` terminated with an error exit status (1)


Command executed:

  add_most_severe_consequence.py --file_in justhusky_svdbquery_vep.vcf.gz --file_out justhusky_sv_csq_research.vcf --variant_csq variant_consequences_v2.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ":
      add_most_severe_consequence: v1.0
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/tecniscan/.nextflow/assets/nf-core/raredisease/bin/add_most_severe_consequence.py", line 192, in <module>
      sys.exit(main())
    File "/home/tecniscan/.nextflow/assets/nf-core/raredisease/bin/add_most_severe_consequence.py", line 188, in main
      write_csq_annotated_vcf(in_vcf, out_vcf, var_csq)
    File "/home/tecniscan/.nextflow/assets/nf-core/raredisease/bin/add_most_severe_consequence.py", line 142, in write_csq_annotated_vcf
      mscsq = construct_most_severe_consequence_info(line, allele_ind, csq_ind, hgnc_ind, var_csq)
    File "/home/tecniscan/.nextflow/assets/nf-core/raredisease/bin/add_most_severe_consequence.py", line 75, in construct_most_severe_consequence_info
      transcripts, allele_ind, csq_ind, hgnc_ind, var_csq
  UnboundLocalError: local variable 'transcripts' referenced before assignment

Work dir:
  /home/tecniscan/Data/raredisease_test/work/3f/72d00dc5d134c5022c49a5a54582b9

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

the .command.sh file is

#!/bin/bash -euo pipefail
add_most_severe_consequence.py --file_in justhusky_svdbquery_vep.vcf.gz --file_out justhusky_sv_csq_research.vcf --variant_csq variant_consequences_v2.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ":
    add_most_severe_consequence: v1.0
    python: $(python --version | sed 's/Python //g')
END_VERSIONS

And when I manually run it throws:

bin/bash: line 0: /bin/bash: ./.command.sh: Invalid option

I found this possible solution: https://unix.stackexchange.com/questions/533415/invalid-option-name-error-with-shebang-bin-bash-o-pipefail-in-script

The weird thing is that it looks like -euo pipefail (which seems causing the problem) is set up globally for all the scripts, so why is only happening here? If I come out with a solution I'll keep you posted, but nothing so far.