[Gmod-help] RE: [Gmod-gbrowse] Problems with Bio::DB::SeqFeature::Store and gff3
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Thu Sep 11 22:39:27 EDT 2008
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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