Validation report with specification /nfs/users/nfs_s/ss34/new_gff_format.lua

• Features
  • pseudogene
    • …only contains allowed attributes successes 77 failures 0 runtime errors 0
    • …contains a pseudogenic_transcript successes 77 failures 0 runtime errors 0
    • …has only allowed child types successes 77 failures 0 runtime errors 0
    • …appears as a root node successes 77 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 77 failures 0 runtime errors 0
  • CDS
    • …should not have children successes 227 failures 0 runtime errors 0
    • …appears as child of an mRNA successes 227 failures 0 runtime errors 0
    • …only contains allowed attributes successes 227 failures 0 runtime errors 0
  • gap
    • …appears as a root node successes 13 failures 0 runtime errors 0
    • …should not have children successes 13 failures 0 runtime errors 0
    • …only contains allowed attributes successes 13 failures 0 runtime errors 0
  • repeat_unit
    • …appears as a root node successes 32 failures 0 runtime errors 0
    • …should not have children successes 32 failures 0 runtime errors 0
  • repeat_region
    • …appears as a root node successes 24 failures 0 runtime errors 0
    • …should not have children successes 24 failures 0 runtime errors 0
  • pseudogenic_transcript
    • …only contains allowed attributes successes 77 failures 0 runtime errors 0
    • …appears as part of a pseudogene successes 77 failures 0 runtime errors 0
    • …has only allowed child types successes 77 failures 0 runtime errors 0
    • …contains at least one pseudogenic_exon successes 77 failures 0 runtime errors 0
  • pseudogenic_exon
    • …appears as part of a pseudogenic_transcript successes 111 failures 0 runtime errors 0
    • …should not have children successes 111 failures 0 runtime errors 0
    • …only contains allowed attributes successes 111 failures 0 runtime errors 0
  • gene
    • …only contains allowed attributes successes 227 failures 0 runtime errors 0
    • …has consistent strands across all children successes 227 failures 0 runtime errors 0
    • …has only allowed child types successes 227 failures 0 runtime errors 0
    • …appears as a root node successes 227 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 227 failures 0 runtime errors 0
  • mRNA
    • …agrees exactly with CDS/UTR coordinates of its children successes 227 failures 0 runtime errors 0
    • …only contains allowed attributes successes 227 failures 0 runtime errors 0
    • …has a coding sequence >= 3bp successes 227 failures 0 runtime errors 0
    • …has at least one CDS child successes 227 failures 0 runtime errors 0
    • …has only allowed child types successes 227 failures 0 runtime errors 0
    • …has non-partial CDS ending on a stop codon successes 224 failures 3 runtime errors 0
      • ID: 13J3.17:mRNA, file TbruceiLister427.noseq.gff3, line 139
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: Tb427.BES126.15:mRNA, file TbruceiLister427.noseq.gff3, line 838
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: N19B2.195:mRNA, file TbruceiLister427.noseq.gff3, line 597
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: F does not match pattern [*+#]
    • …has non-selenocysteine CDS with no internal stop codons successes 227 failures 0 runtime errors 0
    • …consists of less than 50% Ns successes 227 failures 0 runtime errors 0
    • …appears as part of a gene successes 227 failures 0 runtime errors 0
  • polypeptide
    • …agrees exactly with CDS of >=1 overlapping coding transcripts successes 304 failures 0 runtime errors 0
    • …only contains allowed attributes successes 304 failures 0 runtime errors 0
    • …has a required product attribute successes 303 failures 1 runtime errors 0
      • ID: N19B2.140:pseudogenic_transcript:pep, file TbruceiLister427.noseq.gff3, line 536
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:307: should not be nil but is nil
    • …overlaps the transcript it derives_from successes 304 failures 0 runtime errors 0
    • …must be derived_from a unique mRNA successes 304 failures 0 runtime errors 0
    • …appears as a root node successes 304 failures 0 runtime errors 0
• Regions
• Metadata
• Comments
• Sequences
• Warnings