<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="">Find the hit for GAMO_00029233 and then pull it’s header line out of the Uniprot fasta file. There may be an unexpected formatting difference in that header.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 16, 2015, at 1:53 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" class="">ole.toerresen@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Daniel,<br class="">this is the previous gene, before maker_functional_gff:<br class="">LG08 maker gene 13648888 13656687 . - . ID=GAMO_00029212;Name=GAMO_00029212;Alias=maker-LG08-snap-gene-46.325;<br class="">LG08 maker mRNA 13648888 13656687 . - . ID=GAMO_00029212-RA;Parent=GAMO_00029212;Name=GAMO_00029212-RA;Alias=maker-LG08-snap-gene-46.325-mRNA-1;_AED=0.45;_QI=0|0.83|0.84|1|0.5|0.61|13|1843|351;_eAED=0.45;<br class="">LG08 maker exon 13648888 13648944 . - . ID=GAMO_00029212-RA:exon:9363;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13649295 13649577 . - . ID=GAMO_00029212-RA:exon:9362;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13649816 13651468 . - . ID=GAMO_00029212-RA:exon:9361;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13651736 13651789 . - . ID=GAMO_00029212-RA:exon:9360;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13652270 13652365 . - . ID=GAMO_00029212-RA:exon:9359;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13652643 13652730 . - . ID=GAMO_00029212-RA:exon:9358;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653175 13653212 . - . ID=GAMO_00029212-RA:exon:9357;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653587 13653641 . - . ID=GAMO_00029212-RA:exon:9356;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653764 13653817 . - . ID=GAMO_00029212-RA:exon:9355;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653910 13653974 . - . ID=GAMO_00029212-RA:exon:9354;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13654085 13654164 . - . ID=GAMO_00029212-RA:exon:9353;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13654474 13654828 . - . ID=GAMO_00029212-RA:exon:9352;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13656667 13656687 . - . ID=GAMO_00029212-RA:exon:9351;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13656667 13656687 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13654474 13654828 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13654085 13654164 . - 2 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653910 13653974 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653764 13653817 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653587 13653641 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653175 13653212 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13652643 13652730 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13652270 13652365 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13651736 13651789 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13651319 13651468 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13649816 13651318 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13649295 13649577 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13648888 13648944 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br class="">LG08 maker gene 13786695 13806565 . - . ID=GAMO_00029233;Name=GAMO_00029233;Alias=maker-LG08-snap-gene-46.343;<br class="">LG08 maker mRNA 13786695 13806565 . - . ID=GAMO_00029233-RA;Parent=GAMO_00029233;Name=GAMO_00029233-RA;Alias=maker-LG08-snap-gene-46.343-mRNA-1;_AED=0.47;_QI=173|0.78|0.66|1|0.21|0.26|15|0|301;_eAED=0.47;<br class=""><br class=""></div>After :<br class="">LG08 maker gene 13648888 13656687 . - . ID=GAMO_00029212;Name=GAMO_00029212;Alias=maker-LG08-snap-gene-46.325;Note=Similar to Tmbim1: Protein lifeguard 3 (Mus musculus);<br class="">LG08 maker mRNA 13648888 13656687 . - . ID=GAMO_00029212-RA;Parent=GAMO_00029212;Name=GAMO_00029212-RA;Alias=maker-LG08-snap-gene-46.325-mRNA-1;_AED=0.45;_QI=0|0.83|0.84|1|0.5|0.61|13|1843|351;_eAED=0.45;Note=Similar to Tmbim1: Protein lifeguard 3 (Mus musculus);<br class="">LG08 maker exon 13648888 13648944 . - . ID=GAMO_00029212-RA:exon:9363;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13649295 13649577 . - . ID=GAMO_00029212-RA:exon:9362;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13649816 13651468 . - . ID=GAMO_00029212-RA:exon:9361;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13651736 13651789 . - . ID=GAMO_00029212-RA:exon:9360;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13652270 13652365 . - . ID=GAMO_00029212-RA:exon:9359;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13652643 13652730 . - . ID=GAMO_00029212-RA:exon:9358;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653175 13653212 . - . ID=GAMO_00029212-RA:exon:9357;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653587 13653641 . - . ID=GAMO_00029212-RA:exon:9356;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653764 13653817 . - . ID=GAMO_00029212-RA:exon:9355;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13653910 13653974 . - . ID=GAMO_00029212-RA:exon:9354;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13654085 13654164 . - . ID=GAMO_00029212-RA:exon:9353;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13654474 13654828 . - . ID=GAMO_00029212-RA:exon:9352;Parent=GAMO_00029212-RA;<br class="">LG08 maker exon 13656667 13656687 . - . ID=GAMO_00029212-RA:exon:9351;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13656667 13656687 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13654474 13654828 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13654085 13654164 . - 2 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653910 13653974 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653764 13653817 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653587 13653641 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13653175 13653212 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13652643 13652730 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13652270 13652365 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13651736 13651789 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker CDS 13651319 13651468 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13649816 13651318 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13649295 13649577 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br class="">LG08 maker three_prime_UTR 13648888 13648944 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<div class=""><br class=""></div>Carson, I saw that, but I did use Uniprot/Swiss-prot. A snap of the blast-output used as input here:<br class="">GAMO_00029212-RA sp|Q8BJZ3|LFG3_MOUSE 53.93 280 112 3 81 348 33 307 2e-92 285<br class="">GAMO_00029212-RA sp|Q969X1|LFG3_HUMAN 54.51 288 103 5 76 347 33 308 4e-92 284<br class="">GAMO_00029212-RA sp|Q9BWQ8|LFG2_HUMAN 45.73 328 134 6 44 351 13 316 2e-86 270<br class="">GAMO_00029212-RA sp|Q5R4I4|LFG2_PONAB 45.73 328 134 6 44 351 13 316 3e-86 269<br class="">GAMO_00029212-RA sp|Q1LZ71|LFG2_BOVIN 45.03 322 145 5 44 351 13 316 5e-84 264<br class="">GAMO_00029212-RA sp|O88407|LFG2_RAT 44.65 327 139 6 44 351 13 316 8e-83 261<br class="">GAMO_00029212-RA sp|Q8K097|LFG2_MOUSE 45.16 310 129 5 60 351 31 317 1e-80 255<br class="">GAMO_00029212-RA sp|Q7Z429|LFG1_HUMAN 39.32 351 164 9 32 351 39 371 6e-69 226<br class="">GAMO_00029212-RA sp|Q32L53|LFG1_BOVIN 41.69 343 158 8 29 351 46 366 8e-66 218<br class="">GAMO_00029212-RA sp|Q9ESF4|LFG1_MOUSE 40.43 324 156 8 53 351 34 345 2e-59 201<br class="">GAMO_00029212-RA sp|Q6P6R0|LFG1_RAT 39.71 345 165 11 34 351 20 348 2e-59 201<br class="">GAMO_00029212-RA sp|Q9DA39|LFG4_MOUSE 35.59 222 120 7 142 351 27 237 3e-24 103<br class="">GAMO_00029212-RA sp|Q49P94|GAAP_VACCL 33.47 239 128 9 113 337 1 222 5e-22 97.1<br class="">GAMO_00029233-RA sp|Q2KIK0|SGT1_BOVIN 53.18 299 100 3 5 268 17 310 5e-89 275<br class="">GAMO_00029233-RA sp|B0BN85|SGT1_RAT 51.51 299 104 3 5 268 16 308 5e-86 268<br class="">GAMO_00029233-RA sp|Q9CX34|SGT1_MOUSE 51.51 299 104 3 5 268 16 308 8e-86 267<br class="">GAMO_00029233-RA sp|Q9Y2Z0|SGT1_HUMAN 46.83 331 100 5 5 268 16 337 1e-80 254<br class="">GAMO_00029233-RA sp|Q0JL44|SGT1_ORYSJ 30.75 322 160 4 10 268 16 337 5e-36 137<br class="">GAMO_00029233-RA sp|Q9SUT5|SGT1B_ARATH 27.99 318 171 4 9 268 11 328 3e-35 135<br class="">GAMO_00029233-RA sp|Q9SUR9|SGT1A_ARATH 28.28 297 159 5 24 268 26 320 7e-35 134<br class="">GAMO_00029233-RA sp|Q55ED0|SGT1_DICDI 37.72 167 63 3 138 268 196 357 5e-25 107<div class=""><br class=""></div><div class="">521 genes have had added function before maker_functional_gff choked particular gene GAMO_00029233.</div><div class=""><br class=""></div><div class="">Thank you.</div><div class=""><br class=""></div><div class="">Ole</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 16 December 2015 at 20:37, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" 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" target="_blank" class="">https://groups.google.com/forum/#!searchin/maker-devel/$2Fmaker_functional_gff$20line$2058/maker-devel/cBuQMKTJj2M/aXGnARZ7JhsJ</a>).<div class=""><br class=""></div><div class="">It is caused by the ID from the blast report and input protein fasta. maker_functional_gff is not a generic script that can work on any input, it only works on blast results against Uniprot/Swiss-prot. The script is expecting a very specific header format in both the report and the protein fasta and if it doesn’t see it, then it is missing certain pieces of needed information.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><div class="h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Dec 16, 2015, at 12:27 PM, Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank" class="">dence@genetics.utah.edu</a>> wrote:</div><br class=""><div class="">
<div style="word-wrap:break-word" class="">
Hi Ole, can you send a line for a gene feature that does work?
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Dec 14, 2015, at 12:21 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" target="_blank" class="">ole.toerresen@gmail.com</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Hi,
<div class="">I'm trying to update my annotation with some functional annotations with maker_functional_gff, but get this annoying error:</div>
<div class="">Can't use string ("") as a HASH ref while "strict refs" in use at /cluster/software/VERSIONS/maker-2.31.8/bin/maker_functional_gff line 58, <$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="">
</span></p>
</div>
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