<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>I’m glad you were able to fix it. I’ll check to see why it was failing as well.</div><div><br></div><div>Thanks,</div><div>Carson</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> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, March 14, 2014 at 10:16 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">Subject: </span> Re: Error when running maker2zff script<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Kindly ignore my previous question. I was able to manipulate the scaffold names in the gff file to get maker2zff to work.<div><br></div><div>Thanks</div><div>dhivya</div><div><br><div><div>On Mar 14, 2014, at 10:55 AM, dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">My message got flagged by the maker list again, so I’m forwarding this separately to you. Is there a better way to send biggish files?<div><br></div><div><br></div><div>Thank you</div><div>Dhivya</div><div><br></div><div><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family: Helvetica;"><b>From: </b></span><span style="font-family:'Helvetica';">dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family: Helvetica;"><b>Subject: </b></span><span style="font-family:'Helvetica';"><b>Error when running maker2zff script</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family: Helvetica;"><b>Date: </b></span><span style="font-family:'Helvetica';">March 13, 2014 at 8:35:27 PM CDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family: Helvetica;"><b>To: </b></span><span style="font-family:'Helvetica';">Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br></span></div><br><div>Hi Carson,<br><br>I used gff3_merge to create my gff file from maker output. I've attached it here. But when I run maker2zff on it, I get the following error:<br><br>Can't use an undefined value as an ARRAY reference at /opt/apps/maker/2.30/bin/maker2zff line 177, <GFF> line 7294251.<br><br>It produces an incomplete output file and it looks like it may be running into problems when it encounters scaffold3%2F0. I'm wondering if its having problems with my scaffold names. There seem to be some inconsistencies because it's referred to as scaffold3%F0 and scaffold3/0 in the gff file. It goes through other scaffolds like SCAFFOLD3_873, SCAFFOLD3_95 etc just fine. I did try replacing the scaffold names in the gff file, but still get the same error. Any ideas?<br><br>Substitution command I used, for your reference: sed 's/3\%2F/3_/g' gfffile| sed 's/\//\_/' > mod.gfffile<br><br>Thanks<br>Dhivya<br><br></div></blockquote></div></div></div><span><head.gff.gz></span><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><blockquote type="cite"><div></div></blockquote></div><br></div></blockquote></div><br></div></div></div></span></body></html>