<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 Hui,<div class=""><br class=""></div><div class="">1. Make sure you are not using a very old version of MAKER. Current stable version is 2.31.9</div><div class="">2. If you are using GFF3 input as part of your run, then the issue may be in the input GFF3 file (MAKER gets the coordinates from the file you give it).</div><div class="">3. Delete and rerun the contig in question. The lines you gave in your example are missing columns, which may have just been a cut and paste mistake, but if not, then it’s an IO error - failure to print full line - which just needs to be rerun (can sometimes happen with slow NFS file systems).<br class=""><div>4. Make sure you have current version of BioPerl (current CPAN version and not BioPerl-live).</div><div><br class=""></div><div><br class=""></div><div>The only previous occurrence of a start position issue with MAKER ( <a href="https://groups.google.com/forum/#!searchin/maker-devel/start$20position%7Csort:date/maker-devel/Yzn6XTm2aas/J2IOGyWXbVMJ" class="">https://groups.google.com/forum/#!searchin/maker-devel/start$20position%7Csort:date/maker-devel/Yzn6XTm2aas/J2IOGyWXbVMJ</a> ) involved the use of a very old MAKER installation together with bad installation of some prerequisites.</div><div><br class=""></div><div><br class=""></div><div>Thanks,</div><div>Carson</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 13, 2017, at 2:56 AM, 陈军辉(Junhui Chen) <<a href="mailto:chenjunhui@bgi.com" class="">chenjunhui@bgi.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Dear Dr</span>，<span lang="EN-US" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Gooddays for you.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Recently, we used maker software to annotate our genome. However, we found that some annoted genes utr region was out of the scaffold as following:<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">sc0000223 maker five_prime_UTR 101136 101159<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">sc0000223 0 101142<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Would you like to give us some suggetions and help about this problem?<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Many thanks for your help and suggestions<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Look forward from you.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Best regards<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class="">Yours, hui<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: left; font-size: 10.5pt; font-family: 等线;" class=""><b class=""><span style="font-size: 12pt; font-family: 华文楷体;" class="">陈军辉 信息分析工程师</span></b><span lang="EN-US" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><b class=""><span style="font-family: 楷体;" class="">华大基因股份有限公司<span class="Apple-converted-space"> </span></span></b><span lang="EN-US" style="font-family: 宋体; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span style="font-size: 10pt; font-family: 楷体;" class="">通讯地址：深圳市盐田区洪安三街<span lang="EN-US" class="">21</span>号华大综合园<span lang="EN-US" class="">7</span>栋，<span lang="EN-US" class="">518083</span></span><span lang="EN-US" style="" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span style="font-size: 10pt; font-family: 楷体;" class="">联系电话：<span lang="EN-US" class="">0755-36307095</span></span><span lang="EN-US" style="" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; text-align: justify; font-size: 10.5pt; font-family: 等线;" class=""><span style="font-size: 10pt; font-family: 楷体;" class="">邮箱<span lang="EN-US" class="">:<span class="Apple-converted-space"> </span></span></span><u class=""><span lang="EN-US" style="font-size: 10pt; font-family: 楷体; color: blue; background-color: yellow; background-position: initial initial; background-repeat: initial initial;" class=""><a href="mailto:chenjunhui@genomics.cn" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: blue;" class="">chenjunhui@genomics.cn</span></a></span></u><u class=""><span lang="EN-US" style="font-size: 10pt; font-family: 楷体; color: blue;" class=""><o:p class=""></o:p></span></u></div><div style="margin: 0cm 0cm 0.0001pt; 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