<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div><p class="MsoNormal" style="font-family: Calibri, sans-serif;">The only one that may be a real error is the first one (I'm not sure what it means). You probably need to find them and open them in a viewer like apollo. The rest I would consider warnings (the NCBI tool doesn't like any weirdness or uncertainty). You often have to manually edit things to get NCBI to accept all models without complaining (sometimes even going against real biology). I know some groups use the always_complete=1 option in MAKER to force start and stop codons into every model for example (even though those forced codons are probably false).</p><p class="MsoNormal" style="font-family: Calibri, sans-serif;"><br></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*Not sure about this one --> 4 ERROR: SEQ_FEAT.BadTrailingCharacter<o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*These are partial genes with no stop (usually happen at the edge of contigs or near strings of NNNN) --> 217 ERROR: SEQ_FEAT.NoStop<o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*These are just short introns (intron size is under control of the ab initio predictors) --> 438 ERROR: SEQ_FEAT.ShortIntron</p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*These are partial genes with no start (usually happen at the edge of contigs or near strings of NNNN) --> <span style="font-size: 11pt;">171 ERROR: SEQ_FEAT.StartCodon</span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;"><o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*These are partial genes with no start (usually happen at the edge of contigs or near strings of NNNN) --> 171 ERROR: SEQ_INST.BadProteinStart<o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*Non-cononical splicing (can be produced by the ab initio predictor or suggested by EST evidence) --> 291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor<o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*Non-cononical splicing (can be produced by the ab initio predictor or suggested by EST evidence) --> 648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor<o:p></o:p></p><p class="MsoNormal" style="font-family: Calibri, sans-serif;">*These are just short exons (exon size is under control of the ab initio predictors) --> 118 WARNING: SEQ_FEAT.ShortExon</p></div><div><br></div><div>You probably need to identify examples of models causing each issue, and then look at the in Apollo. Apollo lets you open tbl format and save back to it. I imagine the coordinate change is from NCBI using a 0 based coordinate system as opposed to a 1 based system (I.e. first base is 0 rather than 1). Unfortunately getting everything to go into NCBI is usually a grueling task.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Mack, Brian" <<a href="mailto:Brian.Mack@ARS.USDA.GOV">Brian.Mack@ARS.USDA.GOV</a>><br><span style="font-weight:bold">Date: </span> Thursday, April 17, 2014 at 2:34 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] tbl2asn errors<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal">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 (<a href="http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475">http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475</a>). It seemed to have converted fine, however when I use NCBIs tbl2asn program
I get numerous errors in my errorsummary.val file:<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal"> 4 ERROR: SEQ_FEAT.BadTrailingCharacter<o:p></o:p></p><p class="MsoNormal"> 217 ERROR: SEQ_FEAT.NoStop<o:p></o:p></p><p class="MsoNormal"> 438 ERROR: SEQ_FEAT.ShortIntron<o:p></o:p></p><p class="MsoNormal"> 171 ERROR: SEQ_FEAT.StartCodon<o:p></o:p></p><p class="MsoNormal"> 171 ERROR: SEQ_INST.BadProteinStart<o:p></o:p></p><p class="MsoNormal"> 291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor<o:p></o:p></p><p class="MsoNormal"> 648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor<o:p></o:p></p><p class="MsoNormal"> 118 WARNING: SEQ_FEAT.ShortExon<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">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?<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Thanks,<o:p></o:p></p><p class="MsoNormal">Brian<o:p></o:p></p></div><br><br><br><br>
This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil
or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
</div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>