<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="">MAKER uses GFF3 format which is not the same as GTF. You will need to convert your file to GFF3 format.<div class=""><br class=""></div><div class="">You can try this online tool (I haven’t used it to tell you how well it works) <a href="http://www.sequenceontology.org/cgi-bin/converter.cgi" class="">http://www.sequenceontology.org/cgi-bin/converter.cgi</a> </div><div class=""><br class=""></div><div class="">There are also a number of other resources available when you google "how to convert GTF to GFF3”.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 25, 2020, at 3:17 AM, Zoe Clarke <<a href="mailto:zoe.clarke@utoronto.ca" class="">zoe.clarke@utoronto.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Hello!</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data" id="LPlnk" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data</a> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">--------------------------------------------</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 transcript 1094446 1105585 . + . ID=DIMT1.1;geneID=DIMT1</span><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1094446 1094521 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1094874 1094947 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1095459 1095545 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1097351 1097412 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1097492 1097585 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1097670 1097719 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1098957 1099080 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1099217 1099309 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1100870 1100934 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1101967 1102030 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1103784 1103890 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 exon 1105543 1105585 97.75 + . Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1094446 1094521 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1094874 1094947 . + 2 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1095459 1095545 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1097351 1097412 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1097492 1097585 . + 1 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1097670 1097719 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1098957 1099080 . + 1 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1099217 1099309 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1100870 1100934 . + 0 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1101967 1102030 . + 1 Parent=DIMT1.1</span></div><div class=""><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1103784 1103890 . + 0 Parent=DIMT1.1</span></div><span style="font-size: 10pt;" class="">WCK01_AAF20200214_F8-ctg36 ovaltine_v0.13 CDS 1105543 1105582 . + 1 Parent=DIMT1.1</span><br class=""></div><div class="_EReadonly_1 _EType_OWALinkPreview _Entity _EId_OWALinkPreview"></div>--------------------------------------</div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.</span><br class=""></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?</span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. <span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders<span class="Apple-converted-space"> </span><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important;" class="">(e.g. maker_x6V2y4)</span> in my directory.</span> I notice that some of these temporary files haven't been updated in days - is it okay to delete them?</span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">Thank you so much for your help!</span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">Zoe</span></div><div style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><div id="Signature" class=""><div class=""><div class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">______________________________________</span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">Zoe Clarke</span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">PhD candidate in Computational Biology at U of T</span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">Lab profile: </span><a href="http://baderlab.org/Zoe%20Clarke" class=""><span style="font-size: 10pt;" class="">http://baderlab.org/Zoe%20Clarke</span></a></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="font-size: 10pt;" class="">Personal website: </span><a href="https://zoe-clarke.weebly.com/" class=""><span style="font-size: 10pt;" class="">https://zoe-clarke.weebly.com/</span></a></div></div></div></div><span style="caret-color: rgb(0, 0, 0); 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; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); 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; text-decoration: none; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><a href="mailto:maker-devel@yandell-lab.org" style="font-family: Helvetica; font-size: 12px; 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@yandell-lab.org</a><br style="caret-color: rgb(0, 0, 0); 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; text-decoration: none;" class=""><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Helvetica; font-size: 12px; 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://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></body></html>