<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>The issue was indeed caused by a bug in using the other_gff= file option. Could you place the attached file in .../maker/lib/. Then you can rerun maker to test if it fixes it ('maker -a' for fast rerun without analysis rerun).</div><div><br></div><div>Alternately if you don't feel like rerunning everything, you can also filter out the lines using --> grep -v "ARRAY" file.gff</div><div><br></div><div>Since the other_gff file is not used in any part of the analysis and is just a convenience option that prints any text given to it into the final GFF3 file, then filtering them out is the same as if you would have left other_gff blank when running MAKER. You can then use 'gff3_merge -s tophat.gff merged_genome.gff' to merge the desired extra lines back into your file outside of MAKER.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></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 12:29 PM<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">Subject: </span> Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br></div><div><br></div><div dir="ltr">Hi Carson,<div><br></div><div>I uploaded the files as an archive.</div><div><br></div><div>Thanks</div><div>Michael</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 22, 2014 at 5:04 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">In the base maker.output directory for the job, there will be a file with a .db extension. Could you send that as well? I'm leaning towards this being something odd happening with the GFF3 files used as input. Particularly the other_gff= file. Could you upload this file as well --> /home/michael/data/side/alternaria/maker_annotation/Alternaria-CBS-916.96/tophat.gff3.<br><br>
--Carson<br><div class=""><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></div>Date: Tuesday, April 22, 2014 at 8:56 AM<br><div class="">To: Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>><br></div><div class="">Subject: Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><br></div><div class="">Should be uploading right now...<br><br>
Thanks Michael<br><br><br><br></div><div class="">On Tue, Apr 22, 2014 at 4:46 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>> wrote:<br>
Could you pack up this directory for me --> /84/ED/scaffold3.1/ and upload it here --> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" target="_blank">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a><br><br>
Thanks,<br>
Carson<br><br><br></div>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>><mailto:<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><div class="">Date: Tuesday, April 22, 2014 at 8:43 AM<br></div>To: Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>><br>
Cc: "<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>><mailto:<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>>>" <<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>><mailto:<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><div class="">Subject: Re: [maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'<br><br><br></div><div><div class="h5">On Tue, Apr 22, 2014 at 4:39 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a><mailto:<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>>> wrote:<br>
any<br><br>
Dear Carson,<br><br>
maker -version returns 2.31. Yes, also the individual scaffolds seem to contain ARRAY refs, e.g.<br>
find -name "*gff" | xargs grep "ARRAY":<br><br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x41f6ea0)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xb87d888)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xd343528)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xb12fc48)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xde02488)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x8d4c698)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x447a8a0)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x4390048)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xdbb4e00)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xe3f1790)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0x438d570)<br>
./84/ED/scaffold3.1/theVoid.scaffold3.1/evidence_6.gff:ARRAY(0xae00088<br><br>
Cheers<br>
M<br><br><br><br><br><br>
--<br>
Michael F Seidl, PhD<br>
Research Fellow (Postdoc)<br>
Laboratory of Phytopathology<br>
Wageningen University<br>
P.O. Box 8025, 6700 EE Wageningen<br>
Wageningen Campus, building 107 (Radix)<br>
Droevendaalsesteeg 1, 6708 PB Wageningen<br><br>
Tel.: +31-317-481288<br>
Fax: +31-317-483412<br><br></div></div>Email: <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><div class="">Website: <a href="http://www.php.wur.nl/UK/" target="_blank">http://www.php.wur.nl/UK/</a><br>
Twitter: @MFSeidl<br><br></div><a href="http://www.disclaimer-uk.wur.nl" target="_blank">www.disclaimer-uk.wur.nl</a><<a href="http://www.disclaimer-uk.wur.nl/" target="_blank">http://www.disclaimer-uk.wur.nl/</a>><br><br></blockquote></div><br><br clear="all"><div><br></div>-- <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>