[Gmod-help] Problems with Bio::DB::SeqFeature::Store and gff3
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Thu Sep 11 22:10:30 EDT 2008
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:+Bos+taurus+hypothetical+protein+LOC767882+(LOC767882)%2C+partial+mRNA;Entrez_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:+Bos+taurus+similar+to+FARP2+protein+(LOC781869)%2C+mRNA;Entrez_Gene=781869
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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