[maker-devel] tbl2asn errors

[Mack, Brian]

Hi, I thought I would try asking my question here as NCBI was not able to give me much assistance.  In preparation for submitting to NCBI, I converted my my MAKER gff3 to NCBI tbl format using the gff32tbl script that Carson posted a link to in this thread (http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475). It seemed to have converted fine, however when I use NCBIs tbl2asn program I get numerous errors in my errorsummary.val file:

     4 ERROR:   SEQ_FEAT.BadTrailingCharacter
   217 ERROR:   SEQ_FEAT.NoStop
   438 ERROR:   SEQ_FEAT.ShortIntron
   171 ERROR:   SEQ_FEAT.StartCodon
   171 ERROR:   SEQ_INST.BadProteinStart
   291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor
   648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor
   118 WARNING: SEQ_FEAT.ShortExon

In addition, all of the genes, cds, and mRNA coordinates in the resulting sqn files are decreased by one. For example my tbl file will have gene coordinates of 440869 - 441931, but the sqn file will have 440868 - 441930. Any ideas what might be causing this?

Thanks,
Brian




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