<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;">Hello,<div><br><div>After running Maker, I have many directories since I have many contigs.</div><div><br></div><div>Each directory contains these files :</div><div><div><font color="#606060">.gff </font></div><div><font color="#444444">.maker.augustus.transcripts.fasta </font></div><div><font color="#444444">.maker.augustus_masked.proteins.fasta</font></div><div><font color="#444444">.maker.augustus.proteins.fasta</font></div><div><font color="#444444">.maker.augustus_masked.transcripts.fasta</font></div><div><font color="#444444">.maker.transcripts.fasta</font></div><div><font color="#444444">.maker.trnascan.transcripts.fasta</font></div><div><font color="#444444">.maker.proteins.fasta</font></div><div><font color="#444444">.maker.non_overlapping_ab_initio.transcripts.fasta </font></div><div><font color="#444444">.maker.non_overlapping_ab_initio.proteins.fasta</font></div><div><font color="#444444">run.log</font></div><div><font color="#444444">and the directory theVoid.</font></div><div><br></div></div><div>However, for some contigs, one or several files are missing.</div><div>I have more than 50% of contig directory missing the trnascan file.</div><div>Some are missing also the two files « ..non overlapping.. »</div><div>Some miss even more.</div><div><br></div><div>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>So, my questions are :</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>- why are those files missing ?</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>- is it problematic ? Does it mean something didn’t work well ?</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>- should I rerun Maker on these contigs ?</div><div><br></div><div>Thank you !</div><div><br></div><div>Muriel</div></div></body></html>