<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>In your MAKER STDERR (printed to screen or captured as part of run), search for the word ERROR. That will give a more specific explanation as to why it is failing. If you did not capture this on your first run, you may need to redirect it to a file on a retry.</div><div><br></div><div>Example --> maker 2> error.log</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Bérénice Benayoun <<a href="mailto:benayoun@stanford.edu">benayoun@stanford.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, July 5, 2013 5:35 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] FAILED contigs<br></div><div><br></div>Hi maker development team,<br><div class="gmail_quote"><div><br></div><div>sorry to bother you again.</div><div><br></div><div>I was going through the results, and it seems I have a number of contigs that are consistently failing during the annotation of my genome</div><div>(eg, in the log, I find something like "GapFilledScaffold_3308<span style="white-space:pre-wrap"> </span>maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/<span style="white-space:pre-wrap"> </span>FAILED", and no annotation gets outputted). </div><div><br></div><div>No matter how many times I retry their annotation, they start then fail during. Most of the contigs in my assembly still make it through the pipeline.</div><div><br></div><div>Do you have any idea on why some contigs fails for annotation or any advice on what to do to force maker to produce an output on these ? Is there anything I can do to bypass this issue?</div><div><br></div><div>Thanks so much in advance for your insights on this issue!</div><div><br></div><div>Best,</div><div><br></div><div>Berenice<span class="HOEnZb"><font color="#888888"><br clear="all"><div><br></div></font></span></div></div><div><br></div>-- <br><font>Bérénice A. BENAYOUN, Ph.D.</font><br>
Stanford University/Genetics Department<br><i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>
M312 Alway Building<br>
300, Pasteur Drive<br><span>MC 5120 <br>
Stanford, CA 94305-5120</span><br>USA<br>
Email: <a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>
Web: <a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>