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<div>Thanks Carson.</div>
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<div>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>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>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>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>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>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>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>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>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>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>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>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>
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<div>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>Thanks,</div>
<div><br>
</div>
<div>Tim.</div>
<div>
<p style="font-size: 12px; margin: 0px; font-family: Verdana;">---</p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">The Genome Analysis Centre (TGAC)</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);"><span style="text-decoration: underline; font-size: 10px;"><a href="http://www.tgac.ac.uk/">http://www.tgac.ac.uk/</a></span></p>
<p style="margin: 0px; font-family: Cambria; min-height: 19px;"><span style="font-size: 10px;"><br>
</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">p: +44 1603 450378</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);"><span style="color: rgb(0, 0, 0); font-size: 10px;">e: <a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a></span></p>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, 9 November 2014 00:13<br>
<span style="font-weight:bold">To: </span>Timothy Stitt <<a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a>><br>
<span style="font-weight:bold">Cc: </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>Re: [maker-devel] DBD::SQLite::db do failed errors<br>
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<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.:^*$@!+_?-|] must be escaped in GFF3 with exceptions outlined in the format spec. You mayhave either a ‘ or a “ that must be escaped.</div>
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<div class="">—Carson</div>
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<blockquote type="cite" class="">
<div class="">On Nov 8, 2014, at 6:58 AM, Timothy Stitt (TGAC) <<a href="mailto:Timothy.Stitt@tgac.ac.uk" class="">Timothy.Stitt@tgac.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">Dear Maker Support,</div>
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</div>
<div class="">I'm running Maker v2.31.7 and I'm receiving lots of the following warnings/errors during the run. The errors don't seem to prevent the calculation from completing so I was just wondering how I can avoid getting them?</div>
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<div class=""><snip></div>
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<div class="">STATUS: Setting up database for any GFF3 input...</div>
<div class="">DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$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>
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<div class="">…</div>
<div class=""></snip></div>
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<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>
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