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

• Features
  • pseudogene
    • …only contains allowed attributes successes 66 failures 0 runtime errors 0
    • …contains a pseudogenic_transcript successes 66 failures 0 runtime errors 0
    • …has only allowed child types successes 66 failures 0 runtime errors 0
    • …appears as a root node successes 66 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 66 failures 0 runtime errors 0
  • CDS
    • …should not have children successes 8189 failures 0 runtime errors 0
    • …appears as child of an mRNA successes 8189 failures 0 runtime errors 0
    • …only contains allowed attributes successes 8189 failures 0 runtime errors 0
  • mRNA
    • …agrees exactly with CDS/UTR coordinates of its children successes 8173 failures 0 runtime errors 0
    • …only contains allowed attributes successes 8173 failures 0 runtime errors 0
    • …has a coding sequence >= 3bp successes 8173 failures 0 runtime errors 0
    • …has at least one CDS child successes 8173 failures 0 runtime errors 0
    • …has only allowed child types successes 8173 failures 0 runtime errors 0
    • …has non-partial CDS ending on a stop codon successes 8104 failures 66 runtime errors 0
      • ID: LinJ.28.2830:mRNA, file Linfantum.noseq.gff3, line 28848
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: E does not match pattern [*+#]
      • ID: LinJ.26.0870:mRNA, file Linfantum.noseq.gff3, line 24385
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.15.1300a:mRNA, file Linfantum.noseq.gff3, line 11930
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.19.1330:mRNA, file Linfantum.noseq.gff3, line 15957
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.05.0240:mRNA, file Linfantum.noseq.gff3, line 2827
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: G does not match pattern [*+#]
      • ID: LinJ.12.0050:mRNA, file Linfantum.noseq.gff3, line 9060
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.03.0770:mRNA, file Linfantum.noseq.gff3, line 1813
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.07.0640:mRNA, file Linfantum.noseq.gff3, line 4638
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.21.0910:mRNA, file Linfantum.noseq.gff3, line 17805
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: V does not match pattern [*+#]
      • ID: LinJ.28.2950:mRNA, file Linfantum.noseq.gff3, line 28920
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: V does not match pattern [*+#]
      • ID: LinJ.34.4280:mRNA, file Linfantum.noseq.gff3, line 352
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.07.0700:mRNA, file Linfantum.noseq.gff3, line 4674
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.34.1440:mRNA, file Linfantum.noseq.gff3, line 40619
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: LinJ.07.0970:mRNA, file Linfantum.noseq.gff3, line 4840
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.35.2140:mRNA, file Linfantum.noseq.gff3, line 43600
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.04.0920:mRNA, file Linfantum.noseq.gff3, line 2485
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: K does not match pattern [*+#]
      • ID: LinJ.16.1030:mRNA, file Linfantum.noseq.gff3, line 12764
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.25.1290:mRNA, file Linfantum.noseq.gff3, line 23087
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: G does not match pattern [*+#]
      • ID: LinJ.19.1050:mRNA, file Linfantum.noseq.gff3, line 15789
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.20.0460:mRNA, file Linfantum.noseq.gff3, line 16447
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: G does not match pattern [*+#]
      • ID: LinJ.33.2190:mRNA, file Linfantum.noseq.gff3, line 39000
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: S does not match pattern [*+#]
      • ID: LinJ.36.3390:mRNA, file Linfantum.noseq.gff3, line 47638
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.07.0960:mRNA, file Linfantum.noseq.gff3, line 4834
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: V does not match pattern [*+#]
      • ID: LinJ.35.0640:mRNA, file Linfantum.noseq.gff3, line 42699
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.31.3380:mRNA, file Linfantum.noseq.gff3, line 243
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.07.0720:mRNA, file Linfantum.noseq.gff3, line 4686
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.34.0450:mRNA, file Linfantum.noseq.gff3, line 40010
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: P does not match pattern [*+#]
      • ID: LinJ.34.2360:mRNA, file Linfantum.noseq.gff3, line 41165
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: P does not match pattern [*+#]
      • ID: LinJ.26.2120:mRNA, file Linfantum.noseq.gff3, line 25183
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: P does not match pattern [*+#]
      • ID: LinJ.25.0490:mRNA, file Linfantum.noseq.gff3, line 22607
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.21.0160:mRNA, file Linfantum.noseq.gff3, line 17344
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: W does not match pattern [*+#]
      • ID: LinJ.11.1140:mRNA, file Linfantum.noseq.gff3, line 8368
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: E does not match pattern [*+#]
      • ID: LinJ.17.1020:mRNA, file Linfantum.noseq.gff3, line 13815
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: V does not match pattern [*+#]
      • ID: LinJ.27.2510:mRNA, file Linfantum.noseq.gff3, line 303
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: T does not match pattern [*+#]
      • ID: LinJ.17.0160:mRNA, file Linfantum.noseq.gff3, line 13289
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.07.0950:mRNA, file Linfantum.noseq.gff3, line 4828
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.22.0010:mRNA, file Linfantum.noseq.gff3, line 18687
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: LinJ.22.1180:mRNA, file Linfantum.noseq.gff3, line 19383
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: T does not match pattern [*+#]
      • ID: LinJ.14.1600:mRNA, file Linfantum.noseq.gff3, line 213
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: E does not match pattern [*+#]
      • ID: LinJ.31.1830:mRNA, file Linfantum.noseq.gff3, line 34296
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: T does not match pattern [*+#]
      • ID: LinJ.36.6570:mRNA, file Linfantum.noseq.gff3, line 49549
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.27.0250:mRNA, file Linfantum.noseq.gff3, line 25706
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: P does not match pattern [*+#]
      • ID: LinJ.36.4590:mRNA, file Linfantum.noseq.gff3, line 48361
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: V does not match pattern [*+#]
      • ID: LinJ.27.0840:mRNA, file Linfantum.noseq.gff3, line 26168
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: M does not match pattern [*+#]
      • ID: LinJ.36.4580:mRNA, file Linfantum.noseq.gff3, line 48355
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: LinJ.10.0010:mRNA, file Linfantum.noseq.gff3, line 6801
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: M does not match pattern [*+#]
      • ID: LinJ.28.0360:mRNA, file Linfantum.noseq.gff3, line 27372
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: W does not match pattern [*+#]
      • ID: LinJ.35.5440:mRNA, file Linfantum.noseq.gff3, line 165
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: E does not match pattern [*+#]
      • ID: LinJ.17.1420:mRNA, file Linfantum.noseq.gff3, line 14055
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.17.0530:mRNA, file Linfantum.noseq.gff3, line 13512
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.15.1660:mRNA, file Linfantum.noseq.gff3, line 219
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: L does not match pattern [*+#]
      • ID: LinJ.27.2470:mRNA, file Linfantum.noseq.gff3, line 27156
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.33.1000:mRNA, file Linfantum.noseq.gff3, line 38286
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: D does not match pattern [*+#]
      • ID: LinJ.26.1260:mRNA, file Linfantum.noseq.gff3, line 24619
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: P does not match pattern [*+#]
      • ID: LinJ.35.0250:mRNA, file Linfantum.noseq.gff3, line 42462
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.34.0720:mRNA, file Linfantum.noseq.gff3, line 40172
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: K does not match pattern [*+#]
      • ID: LinJ.27.2410:mRNA, file Linfantum.noseq.gff3, line 27120
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: N does not match pattern [*+#]
      • ID: LinJ.04.0700:mRNA, file Linfantum.noseq.gff3, line 2353
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: C does not match pattern [*+#]
      • ID: LinJ.28.2450:mRNA, file Linfantum.noseq.gff3, line 28620
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
      • ID: LinJ.28.1140:mRNA, file Linfantum.noseq.gff3, line 27840
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.35.2410:mRNA, file Linfantum.noseq.gff3, line 43762
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.25.2580:mRNA, file Linfantum.noseq.gff3, line 255
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: S does not match pattern [*+#]
      • ID: LinJ.34.0350:mRNA, file Linfantum.noseq.gff3, line 39950
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: R does not match pattern [*+#]
      • ID: LinJ.13.0940:mRNA, file Linfantum.noseq.gff3, line 9750
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: N does not match pattern [*+#]
      • ID: LinJ.28.3260:mRNA, file Linfantum.noseq.gff3, line 29104
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: C does not match pattern [*+#]
      • ID: LinJ.15.1300b:mRNA, file Linfantum.noseq.gff3, line 11936
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:186: A does not match pattern [*+#]
    • …has non-selenocysteine CDS with no internal stop codons successes 8168 failures 4 runtime errors 0
      • ID: LinJ.26.0450:mRNA, file Linfantum.noseq.gff3, line 24131
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:204: MLMQDAFVLLFRSHALSHTYLLFPRLPSADPLPHDVRCATTCVTHHHNGNVVNCTFSSAWPFLLKYLSVPPRRSLSRSSNP*HACSWSSSLSPHASSRSLSHNNCTLLGPKMMRRAIAQPVARRAAAASSALVVAPRQASTVALSVQGLHYVGTGLAAIALGGVGLGIGAIFGCLLIGCARQPNLTKMLFNYAILGFALTEAIGLFALMLAFLMLFS matches pattern [*+#]
      • ID: LinJ.26.1670:mRNA, file Linfantum.noseq.gff3, line 24865
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:204: MATMFAKRGRADYYWSDTEYTHRTRNREMLKAHGAEIKKLYGPDPWLRYLMTPFVLLQIYLGYRAKDMGWPTLLLVGYFVGGTITHSCFLAIHEATHGLCFITPLYNDLYALFVNLVVPVPYAMMFKTYHAEHHRYLGWDGIDSDVPTRFEGRYLSSYAGKFFFLTFQVLFYALRPTVVRTIKFEKLHVMNYVVQLMFNLLVYYFWGWWPLLYFLLCTFLGTSWHPLAGHFISEHFVLTGNGGQETFSYYGPLNWLMWNVGYHVEHHDFPNIPWTRIGKLNTIAPEFYVDLHRTKSWPGTLFDFLLDPNVSLCSRVVRERGSAGREKLLPTSTGRMKAAEPHQGPCLWKKDG*SDLFVVNLISCYSIV matches pattern [*+#]
      • ID: LinJ.35.2070:mRNA, file Linfantum.noseq.gff3, line 43552
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:204: MLGLTSVMQRIRFCLRACAYAETAAAPFACRMRGSHPGLTTCFFAAFLSPLLRSSSSITVCYLVRTFRLRRSTTAPKPASFAIFPLPTHSNASSTPASVPYFGTPAVTSAHRHSITTALLPFQLTQALSISCKRVCFVPQALCAFVSCW*VWHPPHGTGPTRSRPLSPPFSSPLPSVRAWPTSPFSTHSATAVCCCLVVPSASSPFLRVWPLALLPEQVCFSFFFCVRVLLRCCS matches pattern [*+#]
      • ID: LinJ.26.0720:mRNA, file Linfantum.noseq.gff3, line 24295
        • /nfs/users/nfs_s/ss34/new_gff_format.lua:204: MEAACRRLCQGDTSSLPDIVDCIEAGQQAPTGKLGARAYTALATLMLREGVVLRESHASNSGPPSREAFYALRILAVLGARHAQEGHDVKSVLLSLGLQQCRDMILDAYFFLRRRQRYYVIMFVTLLIGVYGCRPQDLLQNATSLNAMTGSTEFGRLSPRPEGQSEFAELIPALPHHTARVAAAAAGCSGGHTSLTAPANHQPHAATSGSGSPLRCAGVQNRGSLLVSIPGTSADLPLQQTRWYRELPRKPISVPYPVNPLYVSAALREGSSDATAAGGMTCDDGDGDRVSLAFQSLVAEIPMTAQFPTPVVLFSVYYGVGCVPRLPTLDDLARLQVWRERKQQEQAPRPPATDSSSRTFLAEHRHGWGSILEAAVQIREPDVAAEGDDPHLFAVRNEMTFVSPNASTVAYHRQCLGSSLLRHYLEEGKLLSWGSSAKGALGQHRQRRRRSTHGLPINATASSDPAGSNAKVGGTAPASVNAKQQCSSSPDASALGSNEGQASLVGGGSPTAGPLVSVSKVPLARGLSTVDTLSETRPGGRSVADQLQVPPSAGWPKATSTASAGALAVSATSLDVTGAAGYVYLPSYVHAAARVAQVACGLAVTYVLTVDGALYSCGRADNGQLGIGECSVRYSDAGVSKLQRVLLKDNERVTRIAAGTACAMALTGDSALYCWGHNVYGQCLTMPEASHVLTPVRLKAGAYKILDVCFGQLFGVLLFDDGVMGTWGVASMLGCNMSGKRLEQSLAPDRCKCSRQIVHLQFATPTPMAAVRAGPWHALAISQKGEVYTWGVGRNGRLGHGTDNSEVKPRLVEGLRSSFVVDASCSNAHSAVLTSTGAVYVFGENSEGQLGLRGRAPRRLPTMVPLPMKAVAVTCAREHTCILLADGDVVACGSYRTCGIGLGYGRQLCAPSRILTNYVTLTLHCGHLQSMAGAVHRRTSMMVVGHSTIEEVSRVSSLIVRSGVRCAGSGAGFLVVLSENNSLVAIGRGERGQLGIGDRMKPNRRDDVTVAAAFREVHIPSDVVIEHVRCGPDFVLALDTSGVVYGWGSNDHRKLCQPADVAQVFSPVRIAAYASERIVQIVCGGTFVVALTADGEVLTHGEAIYCGLGAPTSPTKAKGSDVPVPMRVAGLSDIVAVAAGLHHAVAMTASCSVFAWGVGVLGTGSTADVSDSTLFTSVTPAPVRVALSQTIRSIGCGPNNSFAISDEGELWVWGMNRFGECGMPTSGKGTGIGTGGGALQRLAARQKEGSDAAADHASAIATPTAVARQVRDAAFTGEFGVVVFEDGQVSVSGRIRYGGQRYLLSSFHSIPQPPFSIDVNEPVWRPPTEPRSSFSASLLGSGGGGASAAVATEPCQQGHQGNADAGGASKNDREPSPSSYVGLPAAGKSAMLPTDGQHQHRPQPPSPPRSYVSGMGAAAASPTSARASKSPPHRASPSLPLMTRGRGSPTIPSSRAATIVGEPAPLATPSNPLLSINSPRLGARDATPLDHGHDMMSAYSLPSISGLIPSAQGSMPQAATAVTLGTMDTEDVRSETDSGVYTVDEEAQANLVSSKAYFNSDEYSAPDAGALFSNAEVPSEADAYTPMPLRRTSDGATPPPVRAKTSTVAQARKPLSATWETLDTRAPPMLPLSPDHSAAQAADVGVATASSTATTTRAAAMAQARAQTPSRIHPAQRGPKVRAAATSKLPKPSLSSPPPPSAADERILGIRCFAGWEQICIVMEKYRPSAAEVGMAQTGLQVLLR*TENAVREA matches pattern [*+#]
    • …consists of less than 50% Ns successes 8173 failures 0 runtime errors 0
    • …appears as part of a gene successes 8173 failures 0 runtime errors 0
  • tRNA
    • …only contains allowed attributes successes 67 failures 0 runtime errors 0
    • …should not have children successes 67 failures 0 runtime errors 0
    • …appears as part of a gene successes 67 failures 0 runtime errors 0
  • ncRNA
    • …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
  • snoRNA
    • …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
  • snRNA
    • …only contains allowed attributes successes 8 failures 0 runtime errors 0
    • …should not have children successes 8 failures 0 runtime errors 0
    • …appears as part of a gene successes 8 failures 0 runtime errors 0
  • pseudogenic_transcript
    • …only contains allowed attributes successes 66 failures 0 runtime errors 0
    • …appears as part of a pseudogene successes 66 failures 0 runtime errors 0
    • …has only allowed child types successes 66 failures 0 runtime errors 0
    • …contains at least one pseudogenic_exon successes 66 failures 0 runtime errors 0
  • pseudogenic_exon
    • …appears as part of a pseudogenic_transcript successes 112 failures 0 runtime errors 0
    • …should not have children successes 112 failures 0 runtime errors 0
    • …only contains allowed attributes successes 112 failures 0 runtime errors 0
  • gene
    • …only contains allowed attributes successes 8315 failures 0 runtime errors 0
    • …has consistent strands across all children successes 8315 failures 0 runtime errors 0
    • …has only allowed child types successes 8315 failures 0 runtime errors 0
    • …appears as a root node successes 8315 failures 0 runtime errors 0
    • …contains all child features within its coordinates successes 8315 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
  • polypeptide
    • …agrees exactly with CDS of >=1 overlapping coding transcripts successes 8239 failures 0 runtime errors 0
    • …only contains allowed attributes successes 8239 failures 0 runtime errors 0
    • …has a required product attribute successes 8239 failures 0 runtime errors 0
    • …overlaps the transcript it derives_from successes 8239 failures 0 runtime errors 0
    • …must be derived_from a unique mRNA successes 8239 failures 0 runtime errors 0
    • …appears as a root node successes 8239 failures 0 runtime errors 0
• Regions
• Metadata
• Comments
• Sequences
• Warnings