<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 upload your control files and job input files here--> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div><br></div><div>I'll take a look to see if there is any problem with your job's setup. Also what version of MAKER are you running?</div><div><br></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> Rebecca Harris <<a href="mailto:rbharris@uw.edu">rbharris@uw.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, April 14, 2014 at 7:45 PM<br><span style="font-weight:bold">To: </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> [maker-devel] empty genome.ann/genome.dna<br></div><div><br></div><div dir="ltr">Hi,<div><br></div><div>I recently set up MAKER on a new computer and am having trouble running a dataset that was run successfully on a different computer. After MAKER is finished, I ran gff3_merge and maker2zff and it returns empty genome.ann and genome.dna files. I have tried installing older versions of dependencies and have tinkered with the control files but I still can't figure out what the issue is. The only difference I can find is that the .all.gff file from a successfully run file has lines at the beginning of the file reporting the success of exonerate. On the failing version of maker - these are not reported - it just goes strait to fasta output. However, exonerate appears to work successfully when run outside of the maker pipeline. Any help would be greatly appreciated.</div><div><br></div><div>Thanks!</div><div>Rebecca</div></div>
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