<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>Glad it's working.</div><div><br></div><div>Thanks,</div><div>Carson</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> Wednesday, October 8, 2014 at 2:13 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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] Maker Bio::Root Error<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><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><div>Thanks Carson…that did the trick. The user was able to format his input file correctly and all worked well.</div><div><br></div><div>Great support,</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></div></div></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>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span>Tuesday, 7 October 2014 17:17<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] Maker Bio::Root Error<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px;"><div style="font-family: Calibri, sans-serif;">His file is not formatted correctly. Values should be tab delimited, but in several cases he has leading space characters contaminating the values. He needs to find and remove the contaminating white space. </div><div style="font-family: Calibri, sans-serif;">Here is the GFF3 specification just for reference --> <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>.</div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;">Here is an example perl script that could do this (cut and paste it into a file if you want)--></div><div style="font-family: Calibri, sans-serif;"><br></div><div><div><font face="Courier">#!/usr/bin/perl
</font></div><div><font face="Courier">use strict;</font></div><div><font face="Courier">my $file = shift;</font></div><div><font face="Courier">open(IN, "< $file");</font></div><div><font face="Courier">while(my $line = <IN>){</font></div><div><font face="Courier"> my @F = split(/\t/, $line);</font></div><div><font face="Courier"> chomp($F[-1]);</font></div><div><font face="Courier"> @F = map {s/^\s|\s$//g; $_} @F;</font></div><div><font face="Courier"> print join("\t", @F)."\n";</font></div><div><font face="Courier">}</font></div><div><font face="Courier">close(IN);</font></div></div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;">Then run it as follows --></div><div><font face="Courier">perl fixgff3_script.pl old_file.gff > new_file.gff</font></div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;">Thanks,</div><div style="font-family: Calibri, sans-serif;">Carson</div><div style="font-family: Calibri, sans-serif;"><br></div><div style="font-family: Calibri, sans-serif;"><br></div><span id="OLK_SRC_BODY_SECTION" style="font-family: Calibri, sans-serif;"><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>Tuesday, October 7, 2014 at 1:34 AM<br><span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span>Re: [maker-devel] Maker Bio::Root Error<br></div><div><br></div><div><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>Hi Carson,</div><div><br></div><div>I spoke with the user and it does seem they have some confusion over what is a well-formed GFF3 file (they mention there is no example template for them to copy on the MAKER website). I am attaching the user's GFF3 file. Could you have a quick scan to
determine if they are using an incorrect format?</div><div><br></div><div>Any advice greatly received.</div><div><br></div><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></div></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>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span>Sunday, 5 October 2014 23:58<br><span style="font-weight:bold">To: </span>Timothy Stitt <<a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a>>, "<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] Maker Bio::Root Error<br></div><div><br></div><div><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>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><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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