Custom GFF file failing ivar_variants_to_vcf.py with release 2.5

[afonsoguerra]

Description of the bug

I've been using a custom GFF file, I've added here in attached, when running viralrecon to highlight variants in the NSP12 which is not highlighted by default in the default GFF. This has worked fine up to version 2.4.1, it now fails in version 2.5.

While I have modified some other parameters, I've excluded them and the custom gff is necessary and sufficient to reproduce the issue.

Command used and terminal output

nextflow run nf-core/viralrecon -r 2.5 -profile singularity,test --outdir tttest --gff 'refannot.gff'



Error: 

Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:IVAR_VARIANTS_TO_VCF (SAMPLE2_PE)'

Caused by:
  Process `NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:IVAR_VARIANTS_TO_VCF (SAMPLE2_PE)` terminated with an error exit status (1)

Command executed:

  ivar_variants_to_vcf.py \
      SAMPLE2_PE.tsv \
      SAMPLE2_PE.vcf \
      --fasta nCoV-2019.reference.fasta \
      --ignore_strand_bias \
      > SAMPLE2_PE.variant_counts.log
  
  cat ivar_variants_header_mqc.txt SAMPLE2_PE.variant_counts.log > SAMPLE2_PE.variant_counts_mqc.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:IVAR_VARIANTS_TO_VCF":
      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/xxxx/.nextflow/assets/nf-core/viralrecon/bin/ivar_variants_to_vcf.py", line 577, in <module>
      sys.exit(main())
    File "/home/xxxx/.nextflow/assets/nf-core/viralrecon/bin/ivar_variants_to_vcf.py", line 552, in main
      fe_codon_ref = variants[next(iter(variants))]["ref_codon"]
  StopIteration

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Relevant files

refannot.gff.gz

System information

  N E X T F L O W
  version 22.04.0 build 5697
  created 23-04-2022 18:00 UTC (19:00 BST)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

Linux step.local 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

HPC running singularity
local executor
singularity containers
viralrecon 2.5

[afonsoguerra]

Just to add that I now found a sample that triggers the same error even with the default GFF file. I can't share that data, but it is just making this issue a bit more urgent for me. Can someone have a look or give me some pointers?

Thanks,
Afonso

[drpatelh]

Ping @saramonzon @svarona

[saramonzon]

Yes, we've already fixed that, I have to make a PR!

[afonsoguerra]

Thanks everyone. I have now been working with the dev version for a while and all seems to be working as it should.

[Rohit-Satyam]

@saramonzon I am still getting the same error. I tried to run ivar_variants_to_vcf.py separately on my ivar.tsv file but it terminates.

(temp) python ~/Documents/COVID_Project/nextCov/modules/ivar_variants_to_vcf.py temp.ivar.tsv temp.ivar.vcf -is -f ../00_index/Sars_cov_2.ASM985889v3.dna.toplevel.fa
Traceback (most recent call last):
  File "/home/subudhak/Documents/COVID_Project/nextCov/modules/ivar_variants_to_vcf.py", line 575, in <module>
    sys.exit(main())
  File "/home/subudhak/Documents/COVID_Project/nextCov/modules/ivar_variants_to_vcf.py", line 518, in main
    ) = process_variants(variants, num_collapse)
  File "/home/subudhak/Documents/COVID_Project/nextCov/modules/ivar_variants_to_vcf.py", line 392, in process_variants
    var = next(iter_variants)
StopIteration

Got it working with code in dev branch. Sorry didn't read the @afonsoguerra comment.

[saramonzon]

Yeah! Great to hear, that dev works :)

[drpatelh]

@afonsoguerra @Rohit-Satyam can I confirm that this issue is fixed already by using the code on the dev branch please?

[afonsoguerra]

Yes. There are issues with the code in edge cases, but this particular issue has been resolved. Thank you!

[drpatelh]

Awesome! Thanks for the quick response. Please feel free to submit individual issues for the edge cases you mentioned and we will try to fix in future releases.