<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>Could you check the individual contig GFF3's before merge. Do any of those contain array refs? Also is it exactly 2.31 or the current 2.31.3?</div><div><br></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> Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>><br><span style="font-weight:bold">Date: </span> Tuesday, April 22, 2014 at 8:37 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br></div><div><br></div><div dir="ltr"><div>Hi Carson,<br><br>I am using maker 2.31.<br><br></div>Thanks<br>Michael<br><div> </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 22, 2014 at 4:31 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I've never seen this. What version of MAKER are you using?<br><br>
--Carson<br><br>
From: Michael Seidl <<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a><mailto:<a href="mailto:michael.seidl@wur.nl">michael.seidl@wur.nl</a>>><br>
Date: Tuesday, April 22, 2014 at 8:27 AM<br>
To: <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><mailto:<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>><br>
Subject: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><div><div class="h5"><br>
Hi,<br><br>
I have a question on the post-processing of my maker output. I finished a maker run on a draft genome (231 scaffolds) without an error. To get a merged gff3 I run ~/local_progs/maker/bin/gff3_merge -d master_datastore_index.log. However, I realized that I contains next to gff3 conform output, thousands of lines of array refs, e.g. ARRAY(0x188a8578)). The total number of produced scaffolds is correct, however I have my doubts if I successfully retrieved all annotations...Could you maybe point me to a possible solution...<br><br>
Thanks in advance<br>
Michael<br><br></div></div>_______________________________________________ maker-devel mailing list <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><mailto:<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" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br><br></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><b style="font-size:8px"><font color="#808080"><font face="verdana,sans-serif"><span style="font-size:10px">Michael F Seidl, PhD</span></font></font></b><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Research Fellow (Postdoc)</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Laboratory of Phytopathology</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999" face="verdana,sans-serif"><span style="font-size:10px;background-color:rgb(255,255,255)">Wageningen University</span></font></span></span></div><div><span style="font-size:14px"><span style="font-size:8px"><font color="#999999"><span style="font-size:10px;background-color:rgb(255,255,255)"><font face="verdana,sans-serif"></font></span></font></span></span></div><div><font color="#999999" size="1" face="verdana,sans-serif">P.O. Box 8025, 6700 EE Wageningen<br>Wageningen Campus, building 107 (Radix)<br>Droevendaalsesteeg 1, 6708 PB Wageningen</font></div><div><font face="verdana,sans-serif"><font color="#999999" size="1"></font> </font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Tel.: +31-317-481288</font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Fax: +31-317-483412</font></div><div><font face="verdana,sans-serif"><font color="#999999" size="1"></font> </font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Email: <a href="mailto:michael.seidl@wur.nl" target="_blank">michael.seidl@wur.nl</a></font></div><div><font color="#999999" size="1"><font face="verdana,sans-serif">Website: </font><a href="http://www.php.wur.nl/UK/" target="_blank"><font face="verdana,sans-serif">http://www.php.wur.nl/UK/</font></a></font></div><div><font color="#999999" size="1" face="verdana,sans-serif">Twitter: @MFSeidl</font></div><div><font face="verdana,sans-serif"> </font></div><div><a href="http://www.disclaimer-uk.wur.nl/" target="_blank"><font color="#999999" size="1" face="verdana,sans-serif">www.disclaimer-uk.wur.nl</font></a></div></div></div></span></body></html>