<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="">Hi Marion,<div class=""><br class=""></div><div class="">None of your evidence supported any of the SNAP models, so you got no results. You did have reference SNAP models in both fasta and GFF3 format (matych/match_part features), but those are just for reference.<div class=""><br class=""></div><div class="">You probably have issues with either your mrna.gff or prot.gff files.</div><div class=""><br class=""></div><div class="">You may want to familiarize yourself with how MAKER works and expected output using an online tutorial like the following —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 16, 2016, at 9:09 AM, Marion Dubarry <<a href="mailto:mdubarry@genoscope.cns.fr" class="">mdubarry@genoscope.cns.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Maker,<br class=""><br class="">I have some issue understanding the output of maker. I ran Maker on a chromosome where I already know the number of expected genes (1332) .<br class=""><br class="">1) I ran Maker with mrna.gff and prot.gff files and Snap (est2genome=1 protein2genome=1) and I try also with just Snap, and I obtain the same files, why ? I was expected that with just ab initio or experimental data, the results would have been different !<br class=""><br class="">In the folder /chr3.maker.output/chr3_datastore/50/43/chr3 I have different files :<br class=""> chr3.gff<br class=""> chr3.maker.non_overlapping_ab_initio.transcripts.fasta<br class=""> chr3.maker.snap_masked.transcripts.fasta<br class=""> theVoid.chr3/<br class=""> chr3.maker.non_overlapping_ab_initio.proteins.fasta<br class=""> chr3.maker.snap_masked.proteins.fasta<br class=""> run.log<br class=""><br class="">2) All of fasta files contains 1263 sequences, while the gff file contains 87178 matches. Why there is a so big differences between my files ?<br class="">In my gff file, line with column 2 = "snap_masked" and column 3 = "match" correspond to the 1263 models in fasta files. To what correspond the "repeatmasker" and "repeatrunner" matches ?<br class=""><br class=""><br class="">Thanks in advance,<br class="">Marion<br class=""><br class="">_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></div></blockquote></div><br class=""></div></div></div></body></html>