<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=""><div class=""><font color="#000000" class="">MAKER’s internal logic has not changed at all. The new release is a minimal update to handle newer versions of GeneMark, tRNAScan, RepeatMasker, and Swiss-Prot (slight deviations from historical output formats).</font></div><div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><br class=""></span></div><div class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">*Update to handle most recent tRNAScan output format.</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">*Update to handle most recent GeneMark output format.</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class="">*Update to downstream putative function scripts to handle newer Swiss-Prot FASTA header format</span></font></div><div class=""><font color="#000000" class="">*Some version/configurations of RepeatMasker can report 0 as a start/end coordinate when it should be 1 (0 is out of bounds), so we fix it when we see it.</font></div><div class=""><br class=""></div>—Carson<div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 17, 2020, at 3:42 PM, <a href="mailto:maker-devel-owner@yandell-lab.org" class="">maker-devel-owner@yandell-lab.org</a> wrote:</div><br class="Apple-interchange-newline"><div class="">As list administrator, your authorization is requested for the<br class="">following mailing list posting:<br class=""><br class=""> List: <a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""> From: <a href="mailto:dianad.mosa@gmail.com" class="">dianad.mosa@gmail.com</a><br class=""> Subject: INCONSISTENCY BETWEEN PROTEINS AND GFF<br class=""> Reason: Post by non-member to a members-only list<br class=""><br class="">At your convenience, visit:<br class=""><br class=""> <a href="http://yandell-lab.org/mailman/admindb/maker-devel_yandell-lab.org" class="">http://yandell-lab.org/mailman/admindb/maker-devel_yandell-lab.org</a><br class=""><br class="">to approve or deny the request.<br class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Diana Moreno Santillán <<a href="mailto:dianad.mosa@gmail.com" class="">dianad.mosa@gmail.com</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">INCONSISTENCY BETWEEN PROTEINS AND GFF</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">July 17, 2020 at 3:32:20 PM MDT<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""></span></div><br class=""><br class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">I am using MAKER for mammalian genomes.</div><div class="">I am running 3 rounds for most of them, as it seems to increase completeness according to BUSCO. </div><div class="">The issue is that the round 3 output has inconsistencies. </div><div class=""><br class=""></div><div class="">For example, at the protein.fasta file I have sequences that after performing blast and rename are annotated, but at the gff file are missing, for example:</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">%grep
AnoCau_scaffold_40730 acaudifer_3rd_run_all_maker_proteins_renamed_putative_function.fasta
</div><div class="">augustus_masked-AnoCau_scaffold_40730-processed-gene-0.0-mRNA-1 protein Name:"Similar to IFNL3 Interferon lambda-3 (Homo sapiens OX=9606)" AED:0.28 eAED:0.23 QI:0|0|0|1|1|1|4|0|183 </div><div class=""><br class=""></div><div class="">%grep
AnoCau_scaffold_40730 acaudifer_3rd_run_all_maker_renamed_putative_function.gff</div><div class="">nothing</div><div class=""><br class=""></div><div class="">Why is the sequence present in my proteins file, but not at my gff3 file?</div><div class=""><br class=""></div><div class="">Is worth to notice that when I tried to run maps_id I got:</div><div class="">WARNING: No mapping available for
AnoCau_scaffold_40730
<br class=""></div><div class=""><br class=""></div><div class="">I found that if I use the gff file from previous rounds of Maker as evidence, this could happen, but I haven't found a solution yet. What do you recommend to avoid these changes of names?</div><div class="">Why I have sequences in my protein file but not in my gff file?</div><div class=""><br class=""></div><div class="">Thank you for your attention. </div><div class=""><br class=""></div><div class="">Diana Moreno </div></div>
<br class=""><br class=""><br class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel-request@yandell-lab.org" class="">maker-devel-request@yandell-lab.org</a><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">confirm 2fbcb7f0a71181de1fcea3c9d2bf4e09bbaca6e4</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">July 17, 2020 at 3:42:30 PM MDT<br class=""></span></div><br class=""><br class="">If you reply to this message, keeping the Subject: header intact,<br class="">Mailman will discard the held message. Do this if the message is<br class="">spam. If you reply to this message and include an Approved: header<br class="">with the list password in it, the message will be approved for posting<br class="">to the list. The Approved: header can also appear in the first line<br class="">of the body of the reply.<br class=""><br class=""></div></blockquote></div><br class=""></div></body></html>