<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Actually that is not a GFF3 file. It appears to be GTF which is structured different from GFF3. You would need to convert to GFF3.<div class=""><br class=""></div><div class="">You can try the sequence ontology converter here —> <a href="http://www.sequenceontology.org/cgi-bin/converter.cgi" class="">http://www.sequenceontology.org/cgi-bin/converter.cgi</a></div><div class=""><br class=""></div><div class="">Unfortunately it will not likely be a painless process as GTF files vary so much between sources that one GTF file might not actually be compatible with another GTF file, so you may have to spend some time editing the file for the converter to work.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 10, 2014, at 6:59 AM, Timothy Stitt (TGAC) <<a href="mailto:Timothy.Stitt@tgac.ac.uk" class="">Timothy.Stitt@tgac.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Thanks Carson.</div>
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<div class="">I checked the *.gff files for ' and " symbols. I only observed a bunch of " in one of the files as follows:</div>
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<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>128238<span class="Apple-tab-span" style="white-space:pre">
</span>128710<span class="Apple-tab-span" style="white-space:pre"> </span>339<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>gene_id 0 ; sequence Lus10000040|PACid:23139618 ; gene_orientation +</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>cds<span class="Apple-tab-span" style="white-space:pre"> </span>128645<span class="Apple-tab-span" style="white-space:pre">
</span>128710<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span></div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>128645<span class="Apple-tab-span" style="white-space:pre">
</span>128710<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>insertions 0 ; deletions 0</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>splice5<span class="Apple-tab-span" style="white-space:pre"> </span>128643<span class="Apple-tab-span" style="white-space:pre">
</span>128644<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 1 ; splice_site "GT"</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>intron<span class="Apple-tab-span" style="white-space:pre"> </span>128552<span class="Apple-tab-span" style="white-space:pre">
</span>128644<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 1</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>splice3<span class="Apple-tab-span" style="white-space:pre"> </span>128552<span class="Apple-tab-span" style="white-space:pre">
</span>128553<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 0 ; splice_site "AG"</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>cds<span class="Apple-tab-span" style="white-space:pre"> </span>128442<span class="Apple-tab-span" style="white-space:pre">
</span>128551<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span></div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>128442<span class="Apple-tab-span" style="white-space:pre">
</span>128551<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>insertions 0 ; deletions 0</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>splice5<span class="Apple-tab-span" style="white-space:pre"> </span>128440<span class="Apple-tab-span" style="white-space:pre">
</span>128441<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 2 ; splice_site "GT"</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>intron<span class="Apple-tab-span" style="white-space:pre"> </span>128362<span class="Apple-tab-span" style="white-space:pre">
</span>128441<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 2</div>
<div class="">scaffold16677<span class="Apple-tab-span" style="white-space:pre"> </span>exonerate:protein2genome:local<span class="Apple-tab-span" style="white-space:pre">
</span>splice3<span class="Apple-tab-span" style="white-space:pre"> </span>128362<span class="Apple-tab-span" style="white-space:pre">
</span>128363<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>intron_id 1 ; splice_site "AG"</div>
</div>
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</div>
<div class="">Would these "GT", "AG" etc. strings cause the problem? If so, how should I change them to be correct?</div>
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</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Tim.</div>
<div class=""><div style="font-size: 12px; margin: 0px; font-family: Verdana;" class="">---</div><div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class=""><b class="">Timothy Stitt PhD</b> / Head of Scientific Computing</span></div><div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class="">The Genome Analysis Centre (TGAC)</span></div><div style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);" class=""><span style="text-decoration: underline; font-size: 10px;" class=""><a href="http://www.tgac.ac.uk/" class="">http://www.tgac.ac.uk/</a></span></div><div style="margin: 0px; font-family: Cambria; min-height: 19px;" class=""><span style="font-size: 10px;" class=""><br class="">
</span></div><div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class="">p: +44 1603 450378</span></div><div style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);" class=""><span style="font-size: 10px;" class="">e: <a href="mailto:timothy.stitt@tgac.ac.uk" class="">timothy.stitt@tgac.ac.uk</a></span></div>
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<span style="font-weight:bold" class="">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Sunday, 9 November 2014 00:13<br class="">
<span style="font-weight:bold" class="">To: </span>Timothy Stitt <<a href="mailto:timothy.stitt@tgac.ac.uk" class="">timothy.stitt@tgac.ac.uk</a>><br class="">
<span style="font-weight:bold" class="">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [maker-devel] DBD::SQLite::db do failed errors<br class="">
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<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">It’s caused by one of the characters in your GFF3 file. For example characters NOT in the set [a-zA-Z0-9.:^*$@!+_?-|] must be escaped in GFF3 with exceptions outlined in the format spec. You mayhave either a ‘ or a “ that must be escaped.</div>
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<div class="">—Carson</div>
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<blockquote type="cite" class="">
<div class="">On Nov 8, 2014, at 6:58 AM, Timothy Stitt (TGAC) <<a href="mailto:Timothy.Stitt@tgac.ac.uk" class="">Timothy.Stitt@tgac.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">Dear Maker Support,</div>
<div class=""><br class="">
</div>
<div class="">I'm running Maker v2.31.7 and I'm receiving lots of the following warnings/errors during the run. The errors don't seem to prevent the calculation from completing so I was just wondering how I can avoid getting them?</div>
<div class=""><br class="">
</div>
<div class=""><snip></div>
<div class="">
<div class="">STATUS: Setting up database for any GFF3 input...</div>
<div class="">DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 1.</div>
<div class="">DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 2.</div>
<div class="">DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 3.</div>
</div>
<div class="">…</div>
<div class=""></snip></div>
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</div>
<div class="">Thanks in advance,</div>
<div class=""><br class="">
</div>
<div class="">Tim.</div>
<div class="">
<div style="font-size: 12px; margin: 0px; font-family: Verdana;" class="">---</div>
<div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class=""><b class="">Timothy Stitt PhD</b> / Head of Scientific Computing</span></div>
<div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class="">The Genome Analysis Centre (TGAC)</span></div>
<div style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);" class="">
<span style="text-decoration: underline; font-size: 10px;" class=""><a href="http://www.tgac.ac.uk/" class="">http://www.tgac.ac.uk/</a></span></div>
<div style="margin: 0px; font-family: Cambria; min-height: 19px;" class=""><span style="font-size: 10px;" class=""><br class="">
</span></div>
<div style="margin: 0px; font-family: Verdana;" class=""><span style="font-size: 10px;" class="">p: +44 1603 450378</span></div>
<div style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);" class="">
<span style="font-size: 10px;" class="">e: <a href="mailto:timothy.stitt@tgac.ac.uk" class="">timothy.stitt@tgac.ac.uk</a></span></div>
</div>
</div>
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