PVGNodes with different sugbrpah IDs were collapsed together causing downstream nodes unprocessed

[lydiayliu]

  NXF_WORK=$(pwd)/work \
  nextflow run /hot/users/yiyangliu/project-MissingPeptides-Method/pipelines/pipeline-meta-call-NonCanonicalPeptide/modules/call_NonCanonicalPeptide/../../external/pipeline-call-NonCano
nicalPeptide/main.nf \
      --sample_name CPCG0256 \
      --input_csv input_3.csv \
      --filterFasta null \
      --output_dir $(pwd)/CPCG0256 \
      --entrypoint gvf \
      --call_variant_ncpus 22 \
      --call_variant_memory_GB 45 GB \
      --variant_fasta NO_VARIANT_FASTA \
      -params-file config.json \
      -c /hot/users/yiyangliu/project-MissingPeptides-Method/pipelines/pipeline-meta-call-NonCanonicalPeptide/modules/call_NonCanonicalPeptide/template.config

Command exit status:
  1

Command wrapper:
      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 351, in call_variant_peptide
          results = ray.get([wrapper_remote.remote(d) for d in dispatches])
        File "/usr/local/lib/python3.8/site-packages/ray/_private/client_mode_hook.py", line 105, in wrapper
          return func(*args, **kwargs)
        File "/usr/local/lib/python3.8/site-packages/ray/_private/worker.py", line 2289, in get
          raise value.as_instanceof_cause()
      ray.exceptions.RayTaskError(ValueError): ray::wrapper_remote() (pid=2770, ip=172.17.0.3)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 248, in wrapper_remote
          return call_variant_peptides_wrapper(*dispatch)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 187, in call_variant_peptides_wrapper
          peptides = call_peptide_main(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 401, in call_peptide_main
          return pgraph.call_variant_peptides(blacklist=ref.canonical_peptides)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/PeptideVariantGraph.py", line 788, in call_variant_peptides
          self.call_and_stage_unknown_orf(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/PeptideVariantGraph.py", line 1070, in call_and_stage_unknown_orf
          traversal.pool.add_miscleaved_sequences(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 390, in add_miscleaved_sequences
          for seq, metadata in seqs:
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 235, in join_miscleaved_peptides
          is_valid = self.is_valid_seq(seq, blacklist)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 164, in is_valid_seq
          and SeqUtils.molecular_weight(seq, 'protein') >= min_mw
        File "/usr/local/lib/python3.8/site-packages/Bio/SeqUtils/__init__.py", line 379, in molecular_weight
          raise ValueError(
      ValueError: '*' is not a valid unambiguous letter for protein
      (wrapper_remote pid=2770) [ 2022-11-29 21:35:33 ] Exception raised from ENST00000545339.5
    
    Work dir:
      work/f1/128d5ad1ea8cc576251a54e7a068cc
    
    Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

GVF

/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/CIRCexplorer2/CPCG0256_circularRNA_known.txt.1.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/Fusion/star-fusion-1.9.1/CPCG0256.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/REDItools/CPCG0256_candidates.rmsk.GRCh38_annotated.txt.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/RMATS/CPCG0256_ijc5_sjc5.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/VEP/gencode/gindel/CPCG0256.gencode.tsv.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/VEP/gencode/gsnp/CPCG0256.gencode.tsv.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/VEP/gencode/pindel/CPCG0256.gencode.tsv.s.gvf
/hot/project/disease/ProstateTumor/PRAD-000051-MIAPEP/Parser/VEP/gencode/somaticsniper/CPCG0256.gencode.tsv.s.gvf