variant should not be converted

[lydiayliu]

Command executed:

  set -euo pipefail
  
  NXF_WORK=/scratch \
  nextflow run /hot/users/yiyangliu/project-MissingPeptides-Method/pipelines/pipeline-meta-call-NonCanonicalPeptide/modules/call_NonCanonicalPeptide/main.nf \
      --input_csv input_CPCG0182-CPCG0183-CPCG0184.csv \
      --exprs_table_csv exprs_table_CPCG0182-CPCG0183-CPCG0184.csv \
      --variant_fasta_csv variant_fasta_CPCG0182-CPCG0183-CPCG0184.csv \
      --output_dir pipeline-meta-call-NonCanonicalPeptide-0.0.1 \
      --entrypoint gvf \
      --call_variant_ncpus 16 \
      --call_variant_memory_GB '32 GB' \
      --config_json config.json

Command exit status:
  1

Command output:
      [ 2022-05-31 00:21:01 ] 1000 transcripts processed.
      [ 2022-05-31 00:21:26 ] 2000 transcripts processed.
      [ 2022-05-31 00:21:56 ] 3000 transcripts processed.
      [ 2022-05-31 00:22:12 ] [ !!! moPepGen WARNING !!! ] Hypermutated region detected from graph: 'ENST00000371287.3'. The argument max_variants_per_node = 7 was used to reduce complexity.
       [ 2022-05-31 00:22:33 ] 4000 transcripts processed.
      [ 2022-05-31 00:23:03 ] Exception raised from ENST00000370321.8
      An error has occured during the function execution
      Traceback (most recent call last):
        File "/usr/local/lib/python3.8/site-packages/ppft/__main__.py", line 106, in run
          __result = __f(*__args)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 208, in wrapper
          return call_variant_peptides_wrapper(*dispatch)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 150, in call_variant_peptides_wrapper
          peptides = call_peptide_main(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 345, in call_peptide_main
          dgraph.create_variant_graph(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/ThreeFrameTVG.py", line 907, in create_variant_graph
          variant.to_end_inclusion(self.seq)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/seqvar/VariantRecord.py", line 407, in to_end_inclusion
          raise ValueError(
      ValueError: This variant should not be converted to end inclusion: 77:148 G -> <DEL>

    Command error:
      Traceback (most recent call last):
        File "/usr/local/bin/moPepGen", line 8, in <module>
          sys.exit(main())
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 89, in main
          args.func(args)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 307, in call_variant_peptide
          for peptides in peptide_series:
      TypeError: 'NoneType' object is not iterable
    
    Work dir:
      work/66/0f8dab1f02ec7d6b080d1b00eb0e0c
    
    Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Work dir:
/hot/project/algorithm/moPepGen/CPCGENE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/work/ee/f868ee18099924de00b029873aa457

You can find all the GVF files in the work dir of the meta pipeline

yiyangliu@ip-0A125212:/hot/project/algorithm/moPepGen/CPCGENE/processed/noncanonical-database/call-nonCanonicalPeptide/GRCh38-EBI-GENCODE34/work/ee/f868ee18099924de00b029873aa457$ cat input_CPCG0182-CPCG0183-CPCG0184.csv 
sample_name,path
CPCG0182,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gindel/CPCG0182.gencode.tsv.s.gvf
CPCG0182,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gsnp/CPCG0182.gencode.tsv.s.gvf
CPCG0182,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/pindel/CPCG0182.gencode.tsv.s.gvf
CPCG0182,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/somaticsniper/CPCG0182.gencode.tsv.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/CIRCexplorer2/CPCG0183_circularRNA_known.txt.1.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/Fusion/star-fusion-1.9.1/CPCG0183.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/REDItools/CPCG0183_candidates.rmsk.GRCh38_annotated.txt.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/RMATS/CPCG0183_ijc5_sjc5.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gindel/CPCG0183.gencode.tsv.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gsnp/CPCG0183.gencode.tsv.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/pindel/CPCG0183.gencode.tsv.s.gvf
CPCG0183,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/somaticsniper/CPCG0183.gencode.tsv.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/CIRCexplorer2/CPCG0184_circularRNA_known.txt.1.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/Fusion/star-fusion-1.9.1/CPCG0184.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/REDItools/CPCG0184_candidates.rmsk.GRCh38_annotated.txt.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/RMATS/CPCG0184_ijc5_sjc5.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gindel/CPCG0184.gencode.tsv.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/gsnp/CPCG0184.gencode.tsv.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/pindel/CPCG0184.gencode.tsv.s.gvf
CPCG0184,/hot/users/yiyangliu/MoPepGen/Parser/VEP/gencode/somaticsniper/CPCG0184.gencode.tsv.s.gvf

Not 100% sure how to check which sample went wrong... Could be that I forgot to reparse a dataset?