[Gmod-help] RE: [Gmod-gbrowse] Problems with Bio::DB::SeqFeature::Store and gff3
Lincoln Stein
lincoln.stein at gmail.com
Fri Sep 12 09:58:53 EDT 2008
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.
Lincoln
On Thu, Sep 11, 2008 at 10:39 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:
> Problem solved :-)
> Don pointed out my sequence line was wrong.
>
> Once changed to the following, all was OK.
> ##gff-version 3
> OAR1 test chromosome 1 80000 . + .
> ID=OAR1;Name=OAR1;Sequence=OAR1
>
>
> Though I'm still getting this mysterious error in the logs:
>
> [Fri Sep 12 14:38:44 2008] [error] [client 147.158.129.160]
> 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:
> http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 14:38:44 2008] [error] [client 147.158.129.160]
> 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:
> http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 14:38:44 2008] [error] [client 147.158.129.160]
> 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:
> http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 14:38:44 2008] [error] [client 147.158.129.160]
> 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:
> http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
>
>
>
> > -----Original Message-----
> > From: gmod-gbrowse-bounces at lists.sourceforge.net [mailto:gmod-gbrowse-
> > bounces at lists.sourceforge.net] On Behalf Of Smithies, Russell
> > Sent: Friday, 12 September 2008 2:11 p.m.
> > To: gmod-gbrowse at lists.sourceforge.net; help at gmod.org
> > Subject: [Gmod-gbrowse] Problems with Bio::DB::SeqFeature::Store and gff3
> >
> > I've spent all morning trying to get gff3 data to display after loading
> into a
> > SeqFeature database and I'm getting nowhere :-(
> > We installed the fresh GBrowse 1.69 release yesterday and had to upgrade
> to
> > bioperl-live as the version of Bioperl we were using (also the latest
> release) was
> > too low according to the install script.
> >
> > Our old GBrowse instances using gff2 data and MySQL are still running
> fine so I
> > assume it's not BioPerl that's broken.
> > But when I try to search for anything on our new gff3 GBrowse, I get the
> usual
> > "landmark maned foobar is not recognized" on the webpage.
> > The error logs are full of this rather cryptic message:
> > -------------------------------------------------
> > [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> > Bio::Graphics::BrowserConfig=HASH(0x1742be30) at
> >
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> > line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-
> > bin/gbrowse/dev_oar/?reset=1
> > [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> > Bio::Graphics::BrowserConfig=HASH(0x1742be30) at
> >
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> > line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-
> > bin/gbrowse/dev_oar/?reset=1
> > [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> > Bio::Graphics::BrowserConfig=HASH(0x1742be30) at
> >
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> > line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-
> > bin/gbrowse/dev_oar/?reset=1
> > [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> > Bio::Graphics::BrowserConfig=HASH(0x1742be30) at
> >
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> > line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-
> > bin/gbrowse/dev_oar/?reset=1
> > [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160] Use of
> uninitialized value
> > in split at /var/www/gbrowse/cgi-bin/gbrowse line 1682., referer:
> > http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> > -------------------------------------------------
> >
> > I've kept my config to a minimum to try and debug:
> >
> > -------------------------------------------------
> > [GENERAL]
> > description = DEVELOPMENT OAR true chromosomes
> >
> > db_adaptor = Bio::DB::SeqFeature::Store
> > db_args = -adaptor DBI::mysql
> > -dsn
> > dbi:mysql:database=dev_oar_chromosomes;host=gbrowsemysql
> > user = username
> > pass = password
> >
> > initial landmark = OAR1:76900..77100
> >
> > # examples to show in the introduction
> > examples = OAR1:100..500 XM_001256510 XM_001250379
> >
> > # Web site configuration info
> > stylesheet = /gbrowse/gbrowse.css
> > buttons = /gbrowse/images/buttons
> > tmpimages = /gbrowse/tmp
> >
> > [TRACK DEFAULTS]
> > glyph = generic
> > height = 8
> > fgcolor = black
> > font2color = gray
> > label density = 800
> > bump density = 10000
> > link_target = _blank
> >
> >
> > [Test]
> > feature = mRNA
> > glyph = cds
> > description = 1
> > key = Test
> > citation = test
> >
> ------------------------------------------------------------------------------
> >
> > And the gff3 data looks like this:
> >
> >
> >
> ------------------------------------------------------------------------------
> > ##gff-version 3
> > OAR1 . chromosome 1 80000 . + .
> Sequence
> > OAR1
> > OAR1 btref mRNA 2988 20491 3756 + .
> > ID=XM_001256510;Target=XM_001256510+1+2278;Note=PREDICTED:+Bo
> > s+taurus+hypothetical+protein+LOC767882+(LOC767882)%2C+partial+mRNA;Entre
> > z_Gene=767882;GO=GO:0003723;GO_Term=RNA+binding
> > OAR1 btref exon 2988 3049 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1+62
> > OAR1 btref exon 4092 4204 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+63+175
> > OAR1 btref exon 6060 6219 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+176+335
> > OAR1 btref exon 7066 7175 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+440+549
> > OAR1 btref exon 11913 12119 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+550+756
> > OAR1 btref exon 12367 12582 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+757+972
> > OAR1 btref exon 13003 13209 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+973+1179
> > OAR1 btref exon 13333 13440 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1180+1287
> > OAR1 btref exon 14246 14350 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1288+1392
> > OAR1 btref exon 14626 14704 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1393+1471
> > OAR1 btref exon 15944 16084 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1472+1612
> > OAR1 btref exon 16735 16748 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1618+1631
> > OAR1 btref exon 16751 16834 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1633+1716
> > OAR1 btref exon 16956 17069 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1717+1830
> > OAR1 btref exon 17844 17930 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+1831+1917
> > OAR1 btref exon 20262 20491 3756 + .
> > Parent=XM_001256510;Target=XM_001256510+2049+2278
> > OAR1 btref mRNA 76974 77060 174 - .
> > ID=XM_001250379;Target=XM_001250379+10+100;Note=PREDICTED:+Bo
> > s+taurus+similar+to+FARP2+protein+(LOC781869)%2C+mRNA;Entrez_Gene=7818
> > 69
> > OAR1 btref exon 76974 76977 174 - .
> > Parent=XM_001250379;Target=XM_001250379+97+100
> > OAR1 btref exon 76978 77053 174 - .
> > Parent=XM_001250379;Target=XM_001250379+20+95
> > OAR1 btref exon 77054 77060 174 - .
> > Parent=XM_001250379;Target=XM_001250379+10+16
> >
> ---------------------------------------------------------------------------
> >
> >
> > As far as I can see, the database is loading correctly:
> >
> > ----------------------------------------------
> > [smithiesr at impala oar]$ bp_seqfeature_load.pl --create --verbose --fast
> --user
> > username --password password -dsn
> > 'dbi:mysql:host=gbrowsemysql;database=dev_oar_chromosomes'
> > dev_gff/OAR1.test.gff3
> > loading dev_gff/OAR1.test.gff3...
> >
> > Building object tree... 0.00s
> > Loading bulk data into database... 0.01s
> > load time: 0.07s
> > ------------------------------------------------
> >
> > Any ideas what to try next??
> > Have I overlooked something obvious?
> >
> >
> > Thanx,
> >
> >
> > Russell Smithies
> >
> > Bioinformatics Applications Developer
> > Invermay Research Centre
> > Puddle Alley,
> > Mosgiel,
> > New Zealand
> > www.agresearch.co.nz
> >
> >
> >
> >
> >
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--
Lincoln D. Stein
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>
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