<div dir="ltr">I found the mistake, I used different versions of SwissProt/UniProt for BLASTing and as an option for maker_functional_gff. When I changed to the same version, the error went away.<div><br></div><div>Sad to say, but stuff like different versions of SwissProt/UniProt do accumulate over time a bit...</div><div><br></div><div>Thank you.</div><div><br></div><div>Ole</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 4 January 2016 at 17:04, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Perhaps the easiest way to look at this is if you send us the files. I’m still leaning towards a format error. But it’s the kind of thing where I would need the files to find the specific entry.<span class="HOEnZb"><font color="#888888"><div><br></div><div>—Carson</div></font></span><div><div class="h5"><div><br><div><br></div><div><br><div><blockquote type="cite"><div>On Dec 16, 2015, at 11:32 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" target="_blank">ole.toerresen@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Here's the hits for GAMO_00029233<br>>sp|Q9SUR9|SGT1A_ARATH Protein SGT1 homolog A OS=Arabidopsis thaliana GN=SGT1A PE=1 SV=1<br>>sp|Q9SUT5|SGT1B_ARATH Protein SGT1 homolog B OS=Arabidopsis thaliana GN=SGT1B PE=1 SV=1<br>>sp|Q2KIK0|SGT1_BOVIN Protein SGT1 homolog OS=Bos taurus GN=SUGT1 PE=2 SV=1<br>>sp|Q55ED0|SGT1_DICDI Protein SGT1 homolog OS=Dictyostelium discoideum GN=sugt1 PE=2 SV=1<br>>sp|Q9Y2Z0|SGT1_HUMAN Protein SGT1 homolog OS=Homo sapiens GN=SUGT1 PE=1 SV=3<br>>sp|Q9CX34|SGT1_MOUSE Protein SGT1 homolog OS=Mus musculus GN=Sugt1 PE=1 SV=3<br>>sp|Q0JL44|SGT1_ORYSJ Protein SGT1 homolog OS=Oryza sativa subsp. japonica GN=SGT1 PE=1 SV=1<br>>sp|B0BN85|SGT1_RAT Protein SGT1 homolog OS=Rattus norvegicus GN=Sugt1 PE=2 SV=1<br><div><br></div><div>The bovin is the first hit. I can't really see anything different about that. </div><div><br></div><div>I'm don't know perl that well. Do you have some code which I can use to debug this? In line 58 it tries to access the blast hash with the ID as a key, if I understand this correctly. Either the hash is empty where the key tries to access, or the key is empty. If I could print each ID as it is found, maybe I can find a pattern. And/or print each blast entry when the blast hash is created.</div><div><br></div><div>Thank you.</div><div><br></div><div>Ole</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 16 December 2015 at 21:55, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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.<span><font color="#888888"><div><br></div><div>—Carson</div></font></span><div><div><div><br><div><br></div><div><br><div><blockquote type="cite"><div>On Dec 16, 2015, at 1:53 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" target="_blank">ole.toerresen@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div>Daniel,<br>this is the previous gene, before maker_functional_gff:<br>LG08 maker gene 13648888 13656687 . - . ID=GAMO_00029212;Name=GAMO_00029212;Alias=maker-LG08-snap-gene-46.325;<br>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>LG08 maker exon 13648888 13648944 . - . ID=GAMO_00029212-RA:exon:9363;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13649295 13649577 . - . ID=GAMO_00029212-RA:exon:9362;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13649816 13651468 . - . ID=GAMO_00029212-RA:exon:9361;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13651736 13651789 . - . ID=GAMO_00029212-RA:exon:9360;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13652270 13652365 . - . ID=GAMO_00029212-RA:exon:9359;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13652643 13652730 . - . ID=GAMO_00029212-RA:exon:9358;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653175 13653212 . - . ID=GAMO_00029212-RA:exon:9357;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653587 13653641 . - . ID=GAMO_00029212-RA:exon:9356;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653764 13653817 . - . ID=GAMO_00029212-RA:exon:9355;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653910 13653974 . - . ID=GAMO_00029212-RA:exon:9354;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13654085 13654164 . - . ID=GAMO_00029212-RA:exon:9353;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13654474 13654828 . - . ID=GAMO_00029212-RA:exon:9352;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13656667 13656687 . - . ID=GAMO_00029212-RA:exon:9351;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13656667 13656687 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13654474 13654828 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13654085 13654164 . - 2 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653910 13653974 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653764 13653817 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653587 13653641 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653175 13653212 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13652643 13652730 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13652270 13652365 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13651736 13651789 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13651319 13651468 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13649816 13651318 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13649295 13649577 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13648888 13648944 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br>LG08 maker gene 13786695 13806565 . - . ID=GAMO_00029233;Name=GAMO_00029233;Alias=maker-LG08-snap-gene-46.343;<br>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><br></div>After :<br>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>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>LG08 maker exon 13648888 13648944 . - . ID=GAMO_00029212-RA:exon:9363;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13649295 13649577 . - . ID=GAMO_00029212-RA:exon:9362;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13649816 13651468 . - . ID=GAMO_00029212-RA:exon:9361;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13651736 13651789 . - . ID=GAMO_00029212-RA:exon:9360;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13652270 13652365 . - . ID=GAMO_00029212-RA:exon:9359;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13652643 13652730 . - . ID=GAMO_00029212-RA:exon:9358;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653175 13653212 . - . ID=GAMO_00029212-RA:exon:9357;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653587 13653641 . - . ID=GAMO_00029212-RA:exon:9356;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653764 13653817 . - . ID=GAMO_00029212-RA:exon:9355;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13653910 13653974 . - . ID=GAMO_00029212-RA:exon:9354;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13654085 13654164 . - . ID=GAMO_00029212-RA:exon:9353;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13654474 13654828 . - . ID=GAMO_00029212-RA:exon:9352;Parent=GAMO_00029212-RA;<br>LG08 maker exon 13656667 13656687 . - . ID=GAMO_00029212-RA:exon:9351;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13656667 13656687 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13654474 13654828 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13654085 13654164 . - 2 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653910 13653974 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653764 13653817 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653587 13653641 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13653175 13653212 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13652643 13652730 . - 1 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13652270 13652365 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13651736 13651789 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker CDS 13651319 13651468 . - 0 ID=GAMO_00029212-RA:cds;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13649816 13651318 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13649295 13649577 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<br>LG08 maker three_prime_UTR 13648888 13648944 . - . ID=GAMO_00029212-RA:three_prime_utr;Parent=GAMO_00029212-RA;<div><br></div>Carson, I saw that, but I did use Uniprot/Swiss-prot. A snap of the blast-output used as input here:<br>GAMO_00029212-RA sp|Q8BJZ3|LFG3_MOUSE 53.93 280 112 3 81 348 33 307 2e-92 285<br>GAMO_00029212-RA sp|Q969X1|LFG3_HUMAN 54.51 288 103 5 76 347 33 308 4e-92 284<br>GAMO_00029212-RA sp|Q9BWQ8|LFG2_HUMAN 45.73 328 134 6 44 351 13 316 2e-86 270<br>GAMO_00029212-RA sp|Q5R4I4|LFG2_PONAB 45.73 328 134 6 44 351 13 316 3e-86 269<br>GAMO_00029212-RA sp|Q1LZ71|LFG2_BOVIN 45.03 322 145 5 44 351 13 316 5e-84 264<br>GAMO_00029212-RA sp|O88407|LFG2_RAT 44.65 327 139 6 44 351 13 316 8e-83 261<br>GAMO_00029212-RA sp|Q8K097|LFG2_MOUSE 45.16 310 129 5 60 351 31 317 1e-80 255<br>GAMO_00029212-RA sp|Q7Z429|LFG1_HUMAN 39.32 351 164 9 32 351 39 371 6e-69 226<br>GAMO_00029212-RA sp|Q32L53|LFG1_BOVIN 41.69 343 158 8 29 351 46 366 8e-66 218<br>GAMO_00029212-RA sp|Q9ESF4|LFG1_MOUSE 40.43 324 156 8 53 351 34 345 2e-59 201<br>GAMO_00029212-RA sp|Q6P6R0|LFG1_RAT 39.71 345 165 11 34 351 20 348 2e-59 201<br>GAMO_00029212-RA sp|Q9DA39|LFG4_MOUSE 35.59 222 120 7 142 351 27 237 3e-24 103<br>GAMO_00029212-RA sp|Q49P94|GAAP_VACCL 33.47 239 128 9 113 337 1 222 5e-22 97.1<br>GAMO_00029233-RA sp|Q2KIK0|SGT1_BOVIN 53.18 299 100 3 5 268 17 310 5e-89 275<br>GAMO_00029233-RA sp|B0BN85|SGT1_RAT 51.51 299 104 3 5 268 16 308 5e-86 268<br>GAMO_00029233-RA sp|Q9CX34|SGT1_MOUSE 51.51 299 104 3 5 268 16 308 8e-86 267<br>GAMO_00029233-RA sp|Q9Y2Z0|SGT1_HUMAN 46.83 331 100 5 5 268 16 337 1e-80 254<br>GAMO_00029233-RA sp|Q0JL44|SGT1_ORYSJ 30.75 322 160 4 10 268 16 337 5e-36 137<br>GAMO_00029233-RA sp|Q9SUT5|SGT1B_ARATH 27.99 318 171 4 9 268 11 328 3e-35 135<br>GAMO_00029233-RA sp|Q9SUR9|SGT1A_ARATH 28.28 297 159 5 24 268 26 320 7e-35 134<br>GAMO_00029233-RA sp|Q55ED0|SGT1_DICDI 37.72 167 63 3 138 268 196 357 5e-25 107<div><br></div><div>521 genes have had added function before maker_functional_gff choked particular gene GAMO_00029233.</div><div><br></div><div>Thank you.</div><div><br></div><div>Ole</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 16 December 2015 at 20:37, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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">https://groups.google.com/forum/#!searchin/maker-devel/$2Fmaker_functional_gff$20line$2058/maker-devel/cBuQMKTJj2M/aXGnARZ7JhsJ</a>).<div><br></div><div>It is caused by the ID from the blast report and input protein fasta. maker_functional_gff is not a generic script that can work on any input, it only works on blast results against Uniprot/Swiss-prot. The script is expecting a very specific header format in both the report and the protein fasta and if it doesn’t see it, then it is missing certain pieces of needed information.<div><br></div><div>Thanks,</div><div>Carson</div><div><div><div><br><div><blockquote type="cite"><div>On Dec 16, 2015, at 12:27 PM, Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>> wrote:</div><br><div>
<div style="word-wrap:break-word">
Hi Ole, can you send a line for a gene feature that does work?
<div><br>
</div>
<div><br>
<div>Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330 </div>
<br>
<div>
<blockquote type="cite">
<div>On Dec 14, 2015, at 12:21 PM, Ole Kristian Tørresen <<a href="mailto:ole.toerresen@gmail.com" target="_blank">ole.toerresen@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Hi,
<div>I'm trying to update my annotation with some functional annotations with maker_functional_gff, but get this annoying error:</div>
<div>Can't use string ("") as a HASH ref while "strict refs" in use at /cluster/software/VERSIONS/maker-2.31.8/bin/maker_functional_gff line 58, <$IN> line 108947.</div>
<div><p><span>Line </span>108947 in the input gff is this:</p><p>LG08 maker gene 13786695 13806565 . - . ID=GAMO_00029233;Name=GAMO_00029233;Alias=maker-LG08-snap-gene-46.343;<br>
</p><p>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><span>Any help to trace down this is really appreciated. Do you need any other information?</span></p><p><span>Thank you.</span></p><p>Sincerely,</p><p>Ole Kristian Tørresen</p><p><span><br>
</span></p>
</div>
</div>
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