<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">Might be related to fragmented CDS where the beginning is missing. The offset (phase) might be different than 0. It is 0 when there is the complete start codon. I don’t know how deals gffread with the offset. You can check within the GFF file if the incriminated genes have this kind of CDS offset start. I know that <a class="js-navigation-open Link--primary" title="agat_sp_extract_sequences.pl" data-pjax="#repo-content-pjax-container" href="https://github.com/NBISweden/AGAT/blob/master/bin/agat_sp_extract_sequences.pl" style="box-sizing: border-box; text-decoration: none; caret-color: rgb(234, 247, 255); font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji"; font-size: 14px; white-space: nowrap; color: var(--color-fg-default) !important;">agat_sp_extract_sequences.pl</a> from AGAT (<a href="https://github.com/NBISweden/AGAT" class="">https://github.com/NBISweden/AGAT</a>) is dealing properly with incomplete CDS and first codon with offset. You might give a try to see if it fix the issue. </div><div class=""><br class=""></div><div class="">Best regards, </div><div class=""><br class=""></div><div class=""><div class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div>Jacques Dainat, Ph.D.<br class=""><br class=""></div></div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On 29 Nov 2021, at 05:20, zc y <<a href="mailto:prometheus07.06@gmail.com" class="">prometheus07.06@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Maker developers,<div class="">I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. </div><div class="">In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. </div><div class="">I used the same parameter and evidence in another rice, it don't have the problem.</div><div class="">What should I do?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">thanks,</div><span id="cid:ii_kwk5v1370"><QQ截图20211129121755.png></span><span id="cid:ii_kwk5xyv61"><QQ截图20211129121917.png></span><br class=""></div>
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