<div dir="ltr">There seems to be a debugging statement left in Browser.pm, though I'm not sure how it got there. Open up Browser.pm at the path indicated in the log, find line 587, and there should be a "warn" line. If there is, then put a comment mark in front of it, and accept my sincere apologies.<br>
<br>Lincoln<br><br><div class="gmail_quote">On Thu, Sep 11, 2008 at 10:39 PM, Smithies, Russell <span dir="ltr"><<a href="mailto:Russell.Smithies@agresearch.co.nz">Russell.Smithies@agresearch.co.nz</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Problem solved :-)<br>
Don pointed out my sequence line was wrong.<br>
<br>
Once changed to the following, all was OK.<br>
##gff-version 3<br>
OAR1 test chromosome 1 80000 . + . ID=OAR1;Name=OAR1;Sequence=OAR1<br>
<br>
<br>
Though I'm still getting this mysterious error in the logs:<br>
<br>
[Fri Sep 12 14:38:44 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>] Bio::Graphics::BrowserConfig=HASH(0x12eaee40) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1</a><br>
[Fri Sep 12 14:38:44 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>] Bio::Graphics::BrowserConfig=HASH(0x12eaee40) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1</a><br>
[Fri Sep 12 14:38:44 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>] Bio::Graphics::BrowserConfig=HASH(0x12eaee40) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1</a><br>
[Fri Sep 12 14:38:44 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>] Bio::Graphics::BrowserConfig=HASH(0x12eaee40) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1</a><br>
<div><div></div><div class="Wj3C7c"><br>
<br>
<br>
> -----Original Message-----<br>
> From: <a href="mailto:gmod-gbrowse-bounces@lists.sourceforge.net">gmod-gbrowse-bounces@lists.sourceforge.net</a> [mailto:<a href="mailto:gmod-gbrowse-">gmod-gbrowse-</a><br>
> <a href="mailto:bounces@lists.sourceforge.net">bounces@lists.sourceforge.net</a>] On Behalf Of Smithies, Russell<br>
> Sent: Friday, 12 September 2008 2:11 p.m.<br>
> To: <a href="mailto:gmod-gbrowse@lists.sourceforge.net">gmod-gbrowse@lists.sourceforge.net</a>; <a href="mailto:help@gmod.org">help@gmod.org</a><br>
> Subject: [Gmod-gbrowse] Problems with Bio::DB::SeqFeature::Store and gff3<br>
><br>
> I've spent all morning trying to get gff3 data to display after loading into a<br>
> SeqFeature database and I'm getting nowhere :-(<br>
> We installed the fresh GBrowse 1.69 release yesterday and had to upgrade to<br>
> bioperl-live as the version of Bioperl we were using (also the latest release) was<br>
> too low according to the install script.<br>
><br>
> Our old GBrowse instances using gff2 data and MySQL are still running fine so I<br>
> assume it's not BioPerl that's broken.<br>
> But when I try to search for anything on our new gff3 GBrowse, I get the usual<br>
> "landmark maned foobar is not recognized" on the webpage.<br>
> The error logs are full of this rather cryptic message:<br>
> -------------------------------------------------<br>
> [Fri Sep 12 13:59:38 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>]<br>
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at<br>
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm<br>
> line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-</a><br>
> bin/gbrowse/dev_oar/?reset=1<br>
> [Fri Sep 12 13:59:38 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>]<br>
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at<br>
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm<br>
> line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-</a><br>
> bin/gbrowse/dev_oar/?reset=1<br>
> [Fri Sep 12 13:59:38 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>]<br>
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at<br>
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm<br>
> line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-</a><br>
> bin/gbrowse/dev_oar/?reset=1<br>
> [Fri Sep 12 13:59:38 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>]<br>
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at<br>
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm<br>
> line 587., referer: <a href="http://devgbrowse.agresearch.co.nz/cgi-" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-</a><br>
> bin/gbrowse/dev_oar/?reset=1<br>
> [Fri Sep 12 13:59:38 2008] [error] [client <a href="http://147.158.129.160" target="_blank">147.158.129.160</a>] Use of uninitialized value<br>
> in split at /var/www/gbrowse/cgi-bin/gbrowse line 1682., referer:<br>
> <a href="http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1" target="_blank">http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1</a><br>
> -------------------------------------------------<br>
><br>
> I've kept my config to a minimum to try and debug:<br>
><br>
> -------------------------------------------------<br>
> [GENERAL]<br>
> description = DEVELOPMENT OAR true chromosomes<br>
><br>
> db_adaptor = Bio::DB::SeqFeature::Store<br>
> db_args = -adaptor DBI::mysql<br>
> -dsn<br>
> dbi:mysql:database=dev_oar_chromosomes;host=gbrowsemysql<br>
> user = username<br>
> pass = password<br>
><br>
> initial landmark = OAR1:76900..77100<br>
><br>
> # examples to show in the introduction<br>
> examples = OAR1:100..500 XM_001256510 XM_001250379<br>
><br>
> # Web site configuration info<br>
> stylesheet = /gbrowse/gbrowse.css<br>
> buttons = /gbrowse/images/buttons<br>
> tmpimages = /gbrowse/tmp<br>
><br>
> [TRACK DEFAULTS]<br>
> glyph = generic<br>
> height = 8<br>
> fgcolor = black<br>
> font2color = gray<br>
> label density = 800<br>
> bump density = 10000<br>
> link_target = _blank<br>
><br>
><br>
> [Test]<br>
> feature = mRNA<br>
> glyph = cds<br>
> description = 1<br>
> key = Test<br>
> citation = test<br>
> ------------------------------------------------------------------------------<br>
><br>
> And the gff3 data looks like this:<br>
><br>
><br>
> ------------------------------------------------------------------------------<br>
> ##gff-version 3<br>
> OAR1 . chromosome 1 80000 . + . Sequence<br>
> OAR1<br>
> OAR1 btref mRNA 2988 20491 3756 + .<br>
> ID=XM_001256510;Target=XM_001256510+1+2278;Note=PREDICTED:+Bo<br>
> s+taurus+hypothetical+protein+LOC767882+(LOC767882)%2C+partial+mRNA;Entre<br>
> z_Gene=767882;GO=GO:0003723;GO_Term=RNA+binding<br>
> OAR1 btref exon 2988 3049 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1+62<br>
> OAR1 btref exon 4092 4204 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+63+175<br>
> OAR1 btref exon 6060 6219 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+176+335<br>
> OAR1 btref exon 7066 7175 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+440+549<br>
> OAR1 btref exon 11913 12119 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+550+756<br>
> OAR1 btref exon 12367 12582 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+757+972<br>
> OAR1 btref exon 13003 13209 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+973+1179<br>
> OAR1 btref exon 13333 13440 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1180+1287<br>
> OAR1 btref exon 14246 14350 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1288+1392<br>
> OAR1 btref exon 14626 14704 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1393+1471<br>
> OAR1 btref exon 15944 16084 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1472+1612<br>
> OAR1 btref exon 16735 16748 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1618+1631<br>
> OAR1 btref exon 16751 16834 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1633+1716<br>
> OAR1 btref exon 16956 17069 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1717+1830<br>
> OAR1 btref exon 17844 17930 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+1831+1917<br>
> OAR1 btref exon 20262 20491 3756 + .<br>
> Parent=XM_001256510;Target=XM_001256510+2049+2278<br>
> OAR1 btref mRNA 76974 77060 174 - .<br>
> ID=XM_001250379;Target=XM_001250379+10+100;Note=PREDICTED:+Bo<br>
> s+taurus+similar+to+FARP2+protein+(LOC781869)%2C+mRNA;Entrez_Gene=7818<br>
> 69<br>
> OAR1 btref exon 76974 76977 174 - .<br>
> Parent=XM_001250379;Target=XM_001250379+97+100<br>
> OAR1 btref exon 76978 77053 174 - .<br>
> Parent=XM_001250379;Target=XM_001250379+20+95<br>
> OAR1 btref exon 77054 77060 174 - .<br>
> Parent=XM_001250379;Target=XM_001250379+10+16<br>
> ---------------------------------------------------------------------------<br>
><br>
><br>
> As far as I can see, the database is loading correctly:<br>
><br>
> ----------------------------------------------<br>
> [smithiesr@impala oar]$ bp_seqfeature_load.pl --create --verbose --fast --user<br>
> username --password password -dsn<br>
> 'dbi:mysql:host=gbrowsemysql;database=dev_oar_chromosomes'<br>
> dev_gff/OAR1.test.gff3<br>
> loading dev_gff/OAR1.test.gff3...<br>
><br>
> Building object tree... 0.00s<br>
> Loading bulk data into database... 0.01s<br>
> load time: 0.07s<br>
> ------------------------------------------------<br>
><br>
> Any ideas what to try next??<br>
> Have I overlooked something obvious?<br>
><br>
><br>
> Thanx,<br>
><br>
><br>
> Russell Smithies<br>
><br>
> Bioinformatics Applications Developer<br>
> Invermay Research Centre<br>
> Puddle Alley,<br>
> Mosgiel,<br>
> New Zealand<br>
> <a href="http://www.agresearch.co.nz" target="_blank">www.agresearch.co.nz</a><br>
><br>
><br>
><br>
><br>
><br>
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Attention: The information contained in this message and/or attachments<br>
from AgResearch Limited is intended only for the persons or entities<br>
to which it is addressed and may contain confidential and/or privileged<br>
material. Any review, retransmission, dissemination or other use of, or<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br><br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>416 673-8514<br>Assistant: Stacey Quinn <<a href="mailto:Stacey.Quinn@oicr.on.ca">Stacey.Quinn@oicr.on.ca</a>><br>
<br>Cold Spring Harbor Laboratory<br>1 Bungtown Road<br>Cold Spring Harbor, NY 11724 USA<br>(516) 367-8380 <br>Assistant: Sandra Michelsen <<a href="mailto:michelse@cshl.edu">michelse@cshl.edu</a>><br>
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