<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">If you modified the fasta files to remove N’s etc after they were annotated, then that would generate a mismatch between the GFF3 coordinates and the fasta sequence.<div class=""><br class=""></div><div class="">Have you modified or split contigs in the assembly in any way? I seem to remember you posting an issue about the fasta submission to NCBI previously.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 2, 2017, at 2:46 PM, Daniel Ence <<a href="mailto:dandence@gmail.com" class="">dandence@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">These gene features with the “nonfunctional due to frameshift” indeed do not have other features associated with them in the tbl files. Is this reflected in the gff3 files for these annotations that maker produced? I’m not certain how maker would maker a gene without a CDS or mRNA, but identifying those discrepancies would a place to understand what has happened. <div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Nov 2, 2017, at 4:30 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Daniel,<div class=""><br class=""></div><div class="">This is the mail they sent to me</div><div class=""><br class=""></div><div class=""><span style="font-size:12.800000190734863px" class="">[1] Please remove any N nucleotides from the beginning or end of the sequence.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[2] No feature should begin or end inside a gap. Instead the feature should</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">be made partial at the gap boundary.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[3] Coding regions should not be 5' partial if they begin with the start</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">methionine. If this is an internal methionine int he translation than</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">it is fine if they are partial. Conversely, all coding regions</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">must have a stop codon or be 3' partial.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[4] You have a large number of gene features that are not associated</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">with other features. Please include on these features in the</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">gene description field some description of what the gene would</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">have encoded.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">A feature table example of this is:</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""><41156 >40652 gene</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> gene_desc transposon</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> locus_tag CR513_45338</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> note nonfunctional due to frameshift</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[5] Every coding region must have a corresponding mRNA and in</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">every case the mRNA product name must match exactly that of the</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">CDS feature.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">2 coding regions do not have an mRNA</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">ORIG/combined_1-5000.sqn:CDS cytochrome c oxidase subunit 2 (contig_100:<38458-</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">39198, 40429->40623) CR513_00692</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">ORIG/combined_1-5000.sqn:CDS cytochrome c oxidase subunit 1</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">(contig_100:c>113064-111485, c111245-111221) CR513_00691</span><br style="font-size:12.800000190734863px" class=""></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><font color="#ff0000" class=""><span style="font-size:12.800000190734863px" class="">So I just went to the .tbl file and searched for </span></font><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class="">nonfunctional due to frameshift They are quite much, I have two more .tbl files </font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class="">I used GAG annotation to remove NNN and to add start and stop codon but ncbi still complained. </font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class="">I have ran out of idea</font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class="">Please help me</font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><font color="#ff0000" class=""><br class=""></font></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Thu, Nov 2, 2017 at 9:24 PM, Daniel Ence <span dir="ltr" class=""><<a href="mailto:dandence@gmail.com" target="_blank" class="">dandence@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi, Thank you for sending me your data, but which ones are the offending genes that NCBI is complaining about? Can you identify the problem that NCBI is giving in some subset of the gene features? <div class=""><br class=""></div><div class="">~Daniel</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On Nov 2, 2017, at 4:20 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_4347594927074793327Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><div dir="ltr" class="">Hi Daniel thanks for your reply.<div class=""><br class=""></div><div class="">I have attached my .tbl file</div><div class=""><br class=""></div><div class="">you would see </div><div class=""><div class=""><77753<span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>>77549<span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>gene</div><div class=""><span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>locus_tag<span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>CR513_00193</div><div class=""><span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>gene<span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>AtMg00820</div><div class=""><span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>note<span class="m_4347594927074793327gmail-m_1027200492982373180gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>nonfunctional due to frameshift</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Is another example.</div><div class=""><br class=""></div><div class="">Its becoming frustrating.</div><div class=""><br class=""></div><div class="">I have not posted the two errors before </div><div class=""><span style="font-size:12.800000190734863px" class="">[1] Please remove any N nucleotides from the beginning or end of the sequence.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[2] No feature should begin or end inside a gap. Instead the feature should</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">be made partial at the gap boundary.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[3] Coding regions should not be 5' partial if they begin with the start</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">methionine. If this is an internal methionine int he translation than</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">it is fine if they are partial. Conversely, all coding regions</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">must have a stop codon or be 3' partial.</span><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_4347594927074793327gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/<wbr class="">publications</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Thu, Nov 2, 2017 at 9:08 PM, Daniel Ence <span dir="ltr" class=""><<a href="mailto:dandence@gmail.com" target="_blank" class="">dandence@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi, I think you’ve posted before about issues 1 and 2 from the NCBI. The note for issue 3 from NCBI sounds like there are gene features that don’t have associated transcript, CDS or exon features. I’m not certain how that could be a result from MAKER. It might be something that someone else created (manually or with another tool), and then passed to maker from a GFF file. In the example included in your email, it looks like these offending genes are transposons that have been annotated as genes. If that is the case for the rest of the offending genes, then I would suggest changing the “type” field (column 3) from “gene” to something else, like “transposable_element” perhaps. <div class=""><br class=""></div><div class="">~Daniel</div><div class=""><br class="">
<br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="m_4347594927074793327h5"><div class="">On Nov 2, 2017, at 3:51 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_4347594927074793327m_-3619321683354011860Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_4347594927074793327h5"><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">I am trying to submit my genome i annotated using maker and they sent back this error,</div><div class="">1. <span style="font-size:12.800000190734863px" class="">Please remove any N nucleotides from the beginning or end of the sequence</span></div><div class=""><span style="font-size:12.800000190734863px" class=""> 2.No feature should begin or end inside a gap. Instead the feature should</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">be made partial at the gap boundary.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">[3] Coding regions should not be 5' partial if they begin with the start</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">methionine. If this is an internal methionine int he translation than</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">it is fine if they are partial. Conversely, all coding regions</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">must have a stop codon or be 3' partial.</span></div><div class=""><span style="font-size:12.800000190734863px" class="">You have a large number of gene features that are not associated</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">with other features. Please include on these features in the</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">gene description field some description of what the gene would</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">have encoded.</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class="">A feature table example of this is:</span><br style="font-size:12.800000190734863px" class=""><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""><41156 >40652 gene</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> gene_desc transposon</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> locus_tag CR513_45338</span><br style="font-size:12.800000190734863px" class=""><span style="font-size:12.800000190734863px" class=""> note nonfunctional due to frameshift</span><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">Please how can i use maker to solve this problem?</span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><div class=""><div class="m_4347594927074793327m_-3619321683354011860gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
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</div></div><span id="m_4347594927074793327cid:910208A2-771F-4BA1-BF3E-CF7BF648664A@ufl.edu" class=""><combined_5001-10000.tbl></span></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div>
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