<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=""><div class="">The problem appears to be the multiple ‘|’ characters in your contig names (ChromoV|quiver|quiver). They end up in the gene ID, and since ‘|’ has a special meaning in perl, it creates weird replacement behavior. I’ve attached two scripts that will fix that.</div><div class="">Use them to replace their counterparts in the …/maker/bin/ and .../maker/src/bin/ directories, then rerun all renaming steps on a new gff3 (not the one you already tried to rename). Also you may want to consider changing IDs in the assembly itself before you release it or use it for analysis. You would want to remove the '|quiver|quiver’ tail on every contig. That tail has the potential to open up hidden downstream analysis errors from other tools for the same reasons outlined above, since ‘|’ characters have special meaning.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>