<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>The location of the error is when MAKER tries to read a user provided GFF3 file, and then BioPerl is saying one of the values is invalid. Looking at the single quotes around the value, it appears that there is some contaminating whitespace. There may be other problems with the GFF3 file as well. I could take look if you want.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Timothy Stitt (TGAC)" <<a href="mailto:Timothy.Stitt@tgac.ac.uk">Timothy.Stitt@tgac.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Saturday, October 4, 2014 at 9:14 AM<br><span style="font-weight:bold">To: </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> [maker-devel] Maker Bio::Root Error<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div><div>Dear Maker Developers,</div><div><br></div><div>One of my Maker users is observing the following error when running maker on our systems:</div><div><br></div><div>------------- EXCEPTION: Bio::Root::BadParameter -------------</div><div>MSG: ' 9.1' is not a valid score</div><div>VALUE: 9.1</div><div>STACK: Error::throw</div><div>STACK: Bio::Root::Root::throw /tgac/software/testing/perl_activeperl/5.18.2.1802/x86_64/site/lib/Bio/Root/Root.pm:449</div><div>STACK: Bio::SeqFeature::Generic::score /tgac/software/testing/perl_activeperl/5.18.2.1802/x86_64/site/lib/Bio/SeqFeature/Generic.pm:468</div><div>STACK: GFFDB::_ary_to_features /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/GFFDB.pm:891</div><div>STACK: GFFDB::phathits_on_chunk /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/GFFDB.pm:534</div><div>STACK: Process::MpiChunk::_go /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:756</div><div>STACK: Process::MpiChunk::run /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:341</div><div>STACK: Process::MpiChunk::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiChunk.pm:357</div><div>STACK: Process::MpiTiers::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiTiers.pm:287</div><div>STACK: Process::MpiTiers::run_all /tgac/software/testing/maker/2.31.6/x86_64/bin/../lib/Process/MpiTiers.pm:287</div><div>STACK: /tgac/software/testing/bin/core/../..//maker/2.31.6/x86_64/bin/maker:686</div><div><div>--------------------------------------------------------------</div><div>--> rank=NA, hostname=UV00000010-P002</div><div>ERROR: Failed while doing repeat masking</div></div><div><br></div><div>When the user runs with the '-RM_off' option, everything is fine but fails with the above error when not applying that option. I was just wondering if anyone had any insight into what might be causing this?</div><div><br></div><div>Regards,</div><div><br></div><div>Tim.</div></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></div></div></div>
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