<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><span style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 15px;">maker_functional_gff works with UniProt/Swiss-Prot. The </span><span style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 15px;">uniref-50 headers are different. The script looks for the OS= GN= and PE= tags. You might be able to coerce it into working on the UniRef header by changing Tax= to OS=, </span><font face="Calibri,sans-serif"><span style="font-size: 15px;">RepID= to GN= and then adding a PE= to the end of the header as just a placeholder.</span></font></div><div><font face="Calibri,sans-serif"><span style="font-size: 15px;"><br></span></font></div><div><font face="Calibri,sans-serif"><span style="font-size: 15px;">--Carson</span></font></div><div><font face="Calibri,sans-serif"><span style="font-size: 15px;"><br></span></font></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><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> "Mack, Brian" <<a href="mailto:Brian.Mack@ARS.USDA.GOV">Brian.Mack@ARS.USDA.GOV</a>><br><span style="font-weight:bold">Date: </span> Monday, April 7, 2014 at 6:55 AM<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] maker_functional_gff<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 12 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal">Hi, I am trying to use the maker_functional_gff program to add functional annotations to my maker gff file. I used blastp with the tabular “-outfmt 6” option against the uniprot uniref-50. I put these results in the maker_functional_gff
program using “maker_functional_gff uniref-50 blastp-output maker.gff” but I get the following errors and no updating of the names in my maker gff file:
<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Use of uninitialized value $id in hash element at /home/b/maker/bin/maker_functional_gff line 142, <$IN> line 16924097.<o:p></o:p></p><p class="MsoNormal">Use of uninitialized value $id in hash element at /home/b/maker/bin/maker_functional_gff line 144, <$IN> line 16924097.<o:p></o:p></p><p class="MsoNormal">Can't parse details from FASTA header: >UniRef50_K1R9E3 Uncharacterized protein n=1 Tax=Crassostrea gigas RepID=K1R9E3_CRAGI<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Use of uninitialized value $id in hash element at /home/b/maker/bin/maker_functional_gff line 142, <$IN> line 16924128.<o:p></o:p></p><p class="MsoNormal">Use of uninitialized value $id in hash element at /home/b/maker/bin/maker_functional_gff line 144, <$IN> line 16924128.<o:p></o:p></p><p class="MsoNormal">Can't parse details from FASTA header: >UniRef50_K1R9E4 Transporter n=2 Tax=Mollusca RepID=K1R9E4_CRAGI<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Any ideas of what I’m doing wrong?<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Brian<o:p></o:p></p></div><br><br><br><br>
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