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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal">I’m having an issue with the id mapping part of the maker pipeline. Specifically, when I run the map_gff_ids script, I get no error messages, the script appears to run, but there are no changes to the gff file. This is one of three genomes
that I’m currently annotating, and only this one is having this particular problem. I’ve tried to find any suspect characters or anything amiss with the gff file, but can’t see anything. I’ve recreated the map file multiple times, but that doesn’t fix the
problem, either.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are the commands I used to make the map file and to try to map the ids to the gff:<o:p></o:p></p>
<p class="MsoNormal"><br>
maker_map_ids --prefix Corav.Jeff_ --justify 5 Corav.Jeff.all.gff > Corav.Jeff.all.id.map<o:p></o:p></p>
<p class="MsoNormal">map_gff_ids Corav.Jeff.all.id.map Corav.Jeff.all.gff<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve attached the map file itself, as well as a subset of the gff file.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help with this is much appreciated!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kelly Vining, Ph.D.<o:p></o:p></p>
<p class="MsoNormal">Assistant Professor, Department of Horticulture<o:p></o:p></p>
<p class="MsoNormal">4071 Agriculture and Life Sciences Bldg<o:p></o:p></p>
<p class="MsoNormal">Oregon State University<o:p></o:p></p>
<p class="MsoNormal">Corvallis, Oregon 97331<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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