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

• Features
  • contig
    • …appears as a root node successes 274 failures 0 runtime errors 0
    • …should not have children successes 274 failures 0 runtime errors 0
    • …only contains allowed attributes successes 274 failures 0 runtime errors 0
  • pseudogene
    • …only contains allowed attributes successes 69 failures 0 runtime errors 0
    • …contains a pseudogenic_transcript successes 68 failures 1 runtime errors 0
      • ID: Tbg972.11.1200, file Tbruceigambiense.noseq.gff3, line 49910
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:61: expecting true, not false
    • …has only allowed child types successes 68 failures 0 runtime errors 0
    • …appears as a root node successes 69 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 69 failures 0 runtime errors 0
  • mRNA
    • …agrees exactly with CDS/UTR coordinates of its children successes 9813 failures 0 runtime errors 0
    • …only contains allowed attributes successes 9813 failures 0 runtime errors 0
    • …has a coding sequence >= 3bp successes 9813 failures 0 runtime errors 0
    • …has at least one CDS child successes 9813 failures 0 runtime errors 0
    • …has only allowed child types successes 9813 failures 0 runtime errors 0
    • …has non-partial CDS ending on a stop codon successes 9704 failures 0 runtime errors 0
    • …has non-selenocysteine CDS with no internal stop codons successes 9812 failures 0 runtime errors 0
    • …consists of less than 50% Ns successes 9812 failures 1 runtime errors 0
      • ID: Tbg972.7.8765:mRNA, file Tbruceigambiense.noseq.gff3, line 25437
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:154: 0.74509803921569 is larger than 0.5
    • …appears as part of a gene successes 9813 failures 0 runtime errors 0
  • direct_repeat
    • …appears as a root node successes 2 failures 0 runtime errors 0
    • …should not have children successes 2 failures 0 runtime errors 0
  • ncRNA
    • …only contains allowed attributes successes 22 failures 0 runtime errors 0
    • …should not have children successes 22 failures 0 runtime errors 0
    • …appears as part of a gene successes 22 failures 0 runtime errors 0
  • snoRNA
    • …only contains allowed attributes successes 5 failures 0 runtime errors 0
    • …should not have children successes 5 failures 0 runtime errors 0
    • …appears as part of a gene successes 5 failures 0 runtime errors 0
  • pseudogenic_transcript
    • …only contains allowed attributes successes 68 failures 0 runtime errors 0
    • …appears as part of a pseudogene successes 68 failures 0 runtime errors 0
    • …has only allowed child types successes 68 failures 0 runtime errors 0
    • …contains at least one pseudogenic_exon successes 68 failures 0 runtime errors 0
  • pseudogenic_exon
    • …appears as part of a pseudogenic_transcript successes 106 failures 0 runtime errors 0
    • …should not have children successes 106 failures 0 runtime errors 0
    • …only contains allowed attributes successes 106 failures 0 runtime errors 0
  • repeat_region
    • …appears as a root node successes 44 failures 0 runtime errors 0
    • …should not have children successes 44 failures 0 runtime errors 0
  • polypeptide
    • …agrees exactly with CDS of >=1 overlapping coding transcripts successes 9881 failures 0 runtime errors 0
    • …only contains allowed attributes successes 9882 failures 0 runtime errors 0
    • …has a required product attribute successes 9882 failures 0 runtime errors 0
    • …overlaps the transcript it derives_from successes 9881 failures 1 runtime errors 0
      • ID: Tbg972.11.1200:pep, file Tbruceigambiense.noseq.gff3, line 49908
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:350: 0 is smaller than 0
    • …must be derived_from a unique mRNA successes 9881 failures 0 runtime errors 1
      • ID: Tbg972.11.1200:pep, file Tbruceigambiense.noseq.gff3, line 49908
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:297: should not be nil but is nil
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:299: table index is nil
    • …appears as a root node successes 9882 failures 0 runtime errors 0
  • repeat_unit
    • …appears as a root node successes 4 failures 0 runtime errors 0
    • …should not have children successes 4 failures 0 runtime errors 0
  • gap
    • …appears as a root node successes 264 failures 0 runtime errors 0
    • …should not have children successes 264 failures 0 runtime errors 0
    • …only contains allowed attributes successes 264 failures 0 runtime errors 0
  • rRNA
    • …only contains allowed attributes successes 16 failures 0 runtime errors 0
    • …should not have children successes 16 failures 0 runtime errors 0
    • …appears as part of a gene successes 16 failures 0 runtime errors 0
  • CDS
    • …should not have children successes 9934 failures 0 runtime errors 0
    • …appears as child of an mRNA successes 9932 failures 2 runtime errors 0
      • ID: Tbg972.11.1200:exon:2, file Tbruceigambiense.noseq.gff3, line 49912
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:274: expecting true, not false
      • ID: Tbg972.11.1200:exon:1, file Tbruceigambiense.noseq.gff3, line 49906
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:274: expecting true, not false
    • …only contains allowed attributes successes 9934 failures 0 runtime errors 0
  • gene
    • …only contains allowed attributes successes 9907 failures 0 runtime errors 0
    • …has consistent strands across all children successes 9907 failures 0 runtime errors 0
    • …has only allowed child types successes 9907 failures 0 runtime errors 0
    • …appears as a root node successes 9907 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 9907 failures 0 runtime errors 0
  • snRNA
    • …only contains allowed attributes successes 1 failures 0 runtime errors 0
    • …should not have children successes 1 failures 0 runtime errors 0
    • …appears as part of a gene successes 1 failures 0 runtime errors 0
  • tRNA
    • …only contains allowed attributes successes 50 failures 0 runtime errors 0
    • …should not have children successes 50 failures 0 runtime errors 0
    • …appears as part of a gene successes 50 failures 0 runtime errors 0
• Regions
• Metadata
• Comments
• Sequences
• Warnings