prepare_submission error "This SeqFeat should not be partial"

[kvertacnik]

This is what the error looks like in the annotated_genome.seq-submit.val file:

Error: valid [SEQ_FEAT.PartialProblem] This SeqFeat should not be partial FEATURE: CDS: cytoplasmic phosphatidylinositol transfer protein 1 <2635>  [(lcl|scaffold0001:c15271572-15271522, c15271296-15271148, c15271066-15270978, c15270841-15270834, c15270772-15270701, c15270628-15270530, c15270458-15270303, c15270222-15270013)] [lcl|scaffold0001: delta, dna len= 40839847] -> [gnl|WGS:ZZZZ|ACNGGK_001431-P1]

These are the other messages involving that gene:

Warning: valid [SEQ_FEAT.PartialsInconsistent] Inconsistent: Location= complete, Feature.partial= TRUE FEATURE: mRNA: cytoplasmic phosphatidylinositol transfer protein 1 <2634>  [(lcl|scaffold0001:c15272014-15271884, c15271701-15271522, c15271296-15271148, c15271066-15270978, c15270841-15270834, c15270772-15270701, c15270628-15270530, c15270458-15270303, c15270222-15270013)] [lcl|scaffold0001: delta, dna len= 40839847]

Warning: valid [SEQ_FEAT.PartialsInconsistent] Inconsistent: Location= complete, Feature.partial= TRUE FEATURE: Prot: cytoplasmic phosphatidylinositol transfer protein 1 <10980>  [gnl|WGS:ZZZZ|ACNGGK_001431-P1:1-277] [gnl|WGS:ZZZZ|ACNGGK_001431-P1: raw, aa len= 277]

Warning: valid [SEQ_FEAT.ShortExon] Internal coding region exon is too short at position 15270834-15270841 FEATURE: CDS: cytoplasmic phosphatidylinositol transfer protein 1 <2635>  [(lcl|scaffold0001:c15271572-15271522, c15271296-15271148, c15271066-15270978, c15270841-15270834, c15270772-15270701, c15270628-15270530, c15270458-15270303, c15270222-15270013)] [lcl|scaffold0001: delta, dna len= 40839847] -> [gnl|WGS:ZZZZ|ACNGGK_001431-P1]

Warning: valid [SEQ_FEAT.PartialProblem] When SeqFeat.product is a partial Bioseq, SeqFeat.location should also be partial FEATURE: CDS: cytoplasmic phosphatidylinositol transfer protein 1 <2635>  [(lcl|scaffold0001:c15271572-15271522, c15271296-15271148, c15271066-15270978, c15270841-15270834, c15270772-15270701, c15270628-15270530, c15270458-15270303, c15270222-15270013)] [lcl|scaffold0001: delta, dna len= 40839847] -> [gnl|WGS:ZZZZ|ACNGGK_001431-P1]

In the asn file this is the section that is different compared to other genes:

 partial TRUE,
 location int {
   from 15270012,
   to 15272013,
   strand minus,
   id local str "scaffold0001",
   fuzz-from lim lt
 },

For reference, the same gene in a different species looks like this:

 location int {
   from 7069515,
   to 7071112,
   strand minus,
   id local str "scaffold0014"
 },

I tried removing the partial TRUE, and fuzz-from lim lt lines but that created a new error.

[murphyte]

Hmm, that's unusual.

Please copy out three snippets of ASN:

1. lines after id local id 2635. Everything to the next feature, after the xref block, would be good.

        {
          id local id 2635,
          data cdregion {
            frame one,
            code {
              id 1
            }
          },
          partial TRUE,  <--- do you see this?
          product whole general {
            db "WGS:ZZZZ",
            tag str "ACNGGK_001431-P1"
          },
          location packed-int {
            {
              from 15271521,
              to 15271571,
              strand minus,
              id local str "scaffold0001"
            },
...
            {
              from 15270012,
              to 15270221,
              strand minus,
              id local str "scaffold0001"
            }
          },
          qual {
            {
              qual "orig_transcript_id",
              val "gnl|WGS:ZZZZ|ACNGGK_001431-R1"
            }
          },
          ext {
...
          xref {
...

2. the same for id local id 2634, which will be the corresponding mRNA feature:
3. the ACNGGK_001431-P1 protein, which will look something like this:

    seq {
      id {
        general {
          db "WGS:ZZZZ",
          tag str "ACNGGK_001431-P1"
        }
      },
      descr {
        molinfo {
          biomol peptide,
          completeness complete
        }
      },
      inst {
        repr raw,
        mol aa,
        length 756,
        seq-data iupacaa "MPLEADVNENFVTLCSYRTASDEQAQKQASSIVTKSNQPSAVEIRRVRLSYG
....
      },
      annot {
        {
          desc {
            create-date std {
              year 2025,
              month 9,
              day 22
            }
          },
          data ftable {
            {
              id local id 25860,
              data prot {
                name {
                  "ABC transporter G family member 20-like"
                }
              },
              location int {
                from 0,
                to 755,
                id general {
                  db "WGS:ZZZZ",
                  tag str "ACNGGK_001431-P1"
                }
              }
            }
          }
        }
      }
    },

[kvertacnik]

Apologies if I pulled the wrong lines. Here is a link to the full ASN (OneDrive)

1. lines after id local id 2635

          id local id 2635,
          data cdregion {
            frame one,
            code {
              id 1
            },
            code-break {
              {
                loc int {
                  from 15270012,
                  to 15270014,
                  strand minus,
                  id local str "scaffold0001"
                },
                aa ncbieaa 88
              }
            }
          },
          partial TRUE,
          except TRUE,
          comment "The sequence of the model RefSeq protein was modified
 relative to this genomic sequence to represent the inferred CDS: substituted
 1 base at 1 genomic stop codon",
          product whole general {
            db "WGS:ZZZZ",
            tag str "ACNGGK_001644-P1"
          },
          location mix {
            int {
              from 15271521,
              to 15271571,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15271147,
              to 15271295,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270977,
              to 15271065,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270833,
              to 15270840,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270700,
              to 15270771,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270529,
              to 15270627,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270302,
              to 15270457,
              strand minus,
              id local str "scaffold0001"
            },
            int {
              from 15270012,
              to 15270221,
              strand minus,
              id local str "scaffold0001",
              fuzz-from lim lt
            }
          },
          qual {
            {
              qual "orig_transcript_id",
              val "gnl|WGS:ZZZZ|ACNGGK_001644-R1"
            }
          },
          ext {
            type str "CombinedFeatureUserObjects",
            data {
              {
                label str "TrackingId",
                data int 1844
              },
              {
                label str "ModelEvidence",
                data object {
                  type str "ModelEvidence",
                  data {
                    {
                      label str "Method",
                      data str "Gnomon"
                    },
                    {
                      label str "Contig Name",
                      data str "scaffold0001"
                    },
                    {
                      label str "Contig Gi",
                      data int 0
                    },
                    {
                      label str "Contig Span",
                      num 2,
                      data ints {
                        15270012,
                        15271571
                      }
                    }
                  }
                }
              }
            }
          },
          xref {
            {
              id local id 2633,
              data gene {
                locus "rdgBbeta",
                desc "cytoplasmic phosphatidylinositol transfer protein 1",
                locus-tag "ACNGGK_001644"
              }
            },
            {
              id local id 2634,
              data rna {
                type mRNA
              }
            }
          },
          except-text "low-quality sequence region"
        },

2. the same for id local id 2634

             {
              id local id 2634,
              data rna {
                type mRNA,
                ext name "cytoplasmic phosphatidylinositol transfer protein 1"
              },
              partial TRUE,
              except TRUE,
              location mix {
                int {
                  from 15271883,
                  to 15272013,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15271521,
                  to 15271700,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15271147,
                  to 15271295,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270977,
                  to 15271065,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270833,
                  to 15270840,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270700,
                  to 15270771,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270529,
                  to 15270627,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270302,
                  to 15270457,
                  strand minus,
                  id local str "scaffold0001"
                },
                int {
                  from 15270012,
                  to 15270221,
                  strand minus,
                  id local str "scaffold0001",
                  fuzz-from lim lt
                }
              },
              qual {
                {
                  qual "orig_protein_id",
                  val "gnl|WGS:ZZZZ|ACNGGK_001644-P1"
                },
                {
                  qual "orig_transcript_id",
                  val "gnl|WGS:ZZZZ|ACNGGK_001644-R1"
                }
              },
              ext {
                type str "CombinedFeatureUserObjects",
                data {
                  {
                    label str "TrackingId",
                    data int 1843
                  },
                  {
                    label str "ModelEvidence",
                    data object {
                      type str "ModelEvidence",
                      data {
                        {
                          label str "Method",
                          data str "Gnomon"
                        },
                        {
                          label str "C_term_partial",
                          data bool TRUE
                        },
                        {
                          label str "NMD",
                          data bool FALSE
                        },
                        {
                          label str "avg_base_coverage",
                          data real { 350360992431641, 10, -12 }
                        },
                        {
                          label str "avg_intron_coverage",
                          data real { 215375, 10, -3 }
                        },
                        {
                          label str "coding_propensity",
                          data real { 783102111816406, 10, -13 }
                        },
                        {
                          label str "minimum_alignments_introns_same_species",
                          data int 0
                        },
                        {
                          label str "num_internal_stop_codons",
                          data int 1
                        },
                        {
                          label str "pct_ab_initio",
                          data int 0
                        },
                        {
                          label str "pct_introns_with_transcripts",
                          data real { 875, 10, -1 }
                        },
                        {
                          label str "protein_len",
                          data int 278
                        },
                        {
                          label str "rnaseq_base_coverage",
                          data int 88
                        },
                        {
                          label str "rnaseq_base_coverage_unambiguous",
                          data int 88
                        },
                        {
                          label str "rnaseq_biosamples_introns_full",
                          data int 0
                        },
                        {
                          label str "rnaseq_biosamples_introns_partial",
                          data int 1
                        },
                        {
                          label str "Contig Name",
                          data str "scaffold0001"
                        },
                        {
                          label str "Contig Gi",
                          data int 0
                        },
                        {
                          label str "Contig Span",
                          num 2,
                          data ints {
                            15270012,
                            15272013
                          }
                        },
                        {
                          label str "Counts",
                          data fields {
                            {
                              label str "Protein",
                              data int 16
                            }
                          }
                        }
                      }
                    }
                  },
                  {
                    label str "MrnaProteinLink",
                    data object {
                      type str "MrnaProteinLink",
                      data {
                        {
                          label str "protein seqID",
                          data str "gnl|WGS:ZZZZ|ACNGGK_001644-P1"
                        }
                      }
                    }
                  }
                }
              },
              xref {
                {
                  id local id 2633,
                  data gene {
                    locus "rdgBbeta",
                    desc "cytoplasmic phosphatidylinositol transfer protein 1",
                    locus-tag "ACNGGK_001644"
                  }
                },
                {
                  id local id 2635,
                  data cdregion {
                  }
                }
              },
              except-text "low-quality sequence region"
            },

3. the ACNGGK_001431-P1 protein

    seq {
      id {
        general {
          db "WGS:ZZZZ",
          tag str "ACNGGK_001431-P1"
        }
      },
      descr {
        molinfo {
          biomol peptide,
          completeness no-right
        }
      },
      inst {
        repr raw,
        mol aa,
        length 278,
        seq-data iupacaa "MVLTKEYRICMPLTTEEYRIGQLYMIARHSHEQSDNDEGVEVVENVECDHPD
HGKGQYTEKRIHLSSKLPYWIQSVIPRIFYVTEKAWNYYPFTITVYTCSFIPKFHITIKTRYEDNNGSTENCLGLSPI
ELIHREVDFVDIAYDELPTKHYKAREDPKFFQSKRTGRGPLVEGWRDTMHPIMCSYKLVHASFEVWGMQTRVEDFIHR
CVKDILILGHRQAFAWIDEWYDMTLEDVREYEHRMQAETNEKVRLRNSNNEMPTTPTSPVPKSPTQSRSX"
      },
      annot {
        {
          desc {
            create-date std {
              year 2025,
              month 8,
              day 31
            }
          },
          data ftable {
            {
              id local id 10980,
              data prot {
                name {
                  "cytoplasmic phosphatidylinositol transfer protein 1"
                }
              },
              partial TRUE,
              location int {
                from 0,
                to 277,
                id general {
                  db "WGS:ZZZZ",
                  tag str "ACNGGK_001431-P1"
                },
                fuzz-to lim gt
              }
            }
          }
        }
      }
    },

[murphyte]

Thanks, that's helpful. Has this been processed with prepare_submission from the v0.4.1 image, or the earlier version?
If it's the earlier version, please rerun and let me know if there's a change in results (in terms of validation output, and if you see a diff in the annotation of these 3 features). There's a very unusual and I thought impossible issue with this particular annotation related to low-quality protein prediction. It's fixable, but (a) I'm curious what the current version of prepare_submission does with it because it's a scenario I never thought of, and (b) we'll separately have to go digging to see how this could have happened in the first place.

[kvertacnik]

It was annotated with v0.4.0 and processed with prepare_submission v0.4.1.