<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I’ve seen this exact same error before (<a href="https://groups.google.com/forum/#!searchin/maker-devel/$2Fmaker_functional_gff$20line$2058/maker-devel/cBuQMKTJj2M/aXGnARZ7JhsJ" class="">https://groups.google.com/forum/#!searchin/maker-devel/$2Fmaker_functional_gff$20line$2058/maker-devel/cBuQMKTJj2M/aXGnARZ7JhsJ</a>).<div class=""><br class=""></div><div class="">It is caused by the ID from the blast report and input protein fasta. maker_functional_gff is not a generic script that can work on any input, it only works on blast results against Uniprot/Swiss-prot. The script is expecting a very specific header format in both the report and the protein fasta and if it doesn’t see it, then it is missing certain pieces of needed information.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 16, 2015, at 12:27 PM, Daniel Ence <<a href="mailto:dence@genetics.utah.edu" class="">dence@genetics.utah.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hi Ole, can you send a line for a gene feature that does work?
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<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Dec 14, 2015, at 12:21 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" class="">ole.toerresen@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
<div class="">I'm trying to update my annotation with some functional annotations with maker_functional_gff, but get this annoying error:</div>
<div class="">Can't use string ("") as a HASH ref while "strict refs" in use at /cluster/software/VERSIONS/maker-2.31.8/bin/maker_functional_gff line 58, <$IN> line 108947.</div>
<div class=""><p class=""><span class="">Line </span>108947 in the input gff is this:</p><p class="">LG08 maker gene 13786695 13806565 . - . ID=GAMO_00029233;Name=GAMO_00029233;Alias=maker-LG08-snap-gene-46.343;<br class="">
</p><p class="">It seems like the regexp in line 55 in the maker_functional_gff script doesn't pick up the ID, but I can't see any difference between that line and other similar lines. </p><p class=""><span class="">Any help to trace down this is really appreciated. Do you need any other information?</span></p><p class=""><span class="">Thank you.</span></p><p class="">Sincerely,</p><p class="">Ole Kristian Tørresen</p><p class=""><span class=""><br class="">
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