<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">If there are no trnasscan results for the contig then there will be no trnascan fasta. The same is true for each of the other feature types.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><div class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 4, 2015, at 6:37 AM, Muriel Gros-Balthazard <<a href="mailto:muriel.grosb@gmail.com" class="">muriel.grosb@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=windows-1252" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hello,<div class=""><br class=""><div class="">After running Maker, I have many directories since I have many contigs.</div><div class=""><br class=""></div><div class="">Each directory contains these files :</div><div class=""><div class=""><font color="#606060" class="">.gff </font></div><div class=""><font color="#444444" class="">.maker.augustus.transcripts.fasta </font></div><div class=""><font color="#444444" class="">.maker.augustus_masked.proteins.fasta</font></div><div class=""><font color="#444444" class="">.maker.augustus.proteins.fasta</font></div><div class=""><font color="#444444" class="">.maker.augustus_masked.transcripts.fasta</font></div><div class=""><font color="#444444" class="">.maker.transcripts.fasta</font></div><div class=""><font color="#444444" class="">.maker.trnascan.transcripts.fasta</font></div><div class=""><font color="#444444" class="">.maker.proteins.fasta</font></div><div class=""><font color="#444444" class="">.maker.non_overlapping_ab_initio.transcripts.fasta </font></div><div class=""><font color="#444444" class="">.maker.non_overlapping_ab_initio.proteins.fasta</font></div><div class=""><font color="#444444" class="">run.log</font></div><div class=""><font color="#444444" class="">and the directory theVoid.</font></div><div class=""><br class=""></div></div><div class="">However, for some contigs, one or several files are missing.</div><div class="">I have more than 50% of contig directory missing the trnascan file.</div><div class="">Some are missing also the two files « ..non overlapping.. »</div><div class="">Some miss even more.</div><div class=""><br class=""></div><div class="">However, for all these contigs for which files are missing, I have the gff file and it’s written FINISHED in the log file.</div><div class="">So, my questions are :</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>- why are those files missing ?</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>- is it problematic ? Does it mean something didn’t work well ?</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>- should I rerun Maker on these contigs ?</div><div class=""><br class=""></div><div class="">Thank you !</div><div class=""><br class=""></div><div class="">Muriel</div></div></div>_______________________________________________<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></blockquote></div><br class=""></div></div></div></div></div></body></html>