<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="">You can merge datastore indexes that way. You will need to run them separately (i.e. unmodified location and content from what MAKER gave you), and then merge the fasta and gff3 files afterwards.<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 May 1, 2017, at 7:32 AM, <a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span class=""></span>Dear sir:</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> I' have bben working on genome annotation these days.My process in as below:</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> </div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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; orphans: 2; widows: 2;" class=""> 1. I split my contigs into 300 parts and deal with them <span style="font-family: arial; color: rgb(204, 0, 0); background-color: rgba(0, 0, 0, 0);" class="">simultaneously</span> to speed up my process. </div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> 2. I used my splited-genome, protein, ESTs and RNA-seq to make the first alignment( est2genome=1, <span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: '';" class="">AED_threshold=0.2 </span>). </div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> 3. Merge the maker.*_.master_datastore_index.log to get all the paths of results.</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> 4. gff_merge script to merge all the results in different dirs.</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><br class=""></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> <span class="Apple-converted-space"> </span><b class="">However, there is no results returned. (My genome is about 3GB, but the gff of result is none.)</b></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><b class=""> </b><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">index_all.log.all.gff 1KB</span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span><span style="background-color: window;" class="">index_all.log.all.maker.proteins.fasta 2837KB</span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="background-color: window;" class=""> </span><span style="background-color: window;" class="">index_all.log.all.maker.transcripts.fasta 9866KB</span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="background-color: window;" class=""><br class=""></span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="background-color: window;" class=""><br class=""></span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="background-color: window;" class=""><br class=""></span></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><br class=""></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> Where can the problems take place?</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""> Thanks!</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class="">Yours sincerely.</div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><br class=""></div><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class="">Chao Chao</div><hr size="1" align="left" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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; width: 210px; height: 1px;" class=""><div style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span class=""><div style="margin: 10px; font-family: verdana; font-size: 10pt;" class=""><div class=""><a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a></div></div></span></div><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><span style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: 'Microsoft YaHei UI'; font-size: 14px; 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;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></div></body></html>