[Gmod-gbrowse] [Gmod-help] Gbrowse fails with too many tracks
Scott Cain
scott at scottcain.net
Wed Sep 29 16:29:16 EDT 2010
Hi Grace,
About GBrowse2: the reason you can't find anything is that none of
your features have Name tags. The ID tag is for showing parent-child
relationships in the GFF file, needed for lines like these:
ADVE01000008 GenBank gene 1 492 . - . ID=MettrDRAFT_0987;locus_tag=MettrDRAFT_0987
ADVE01000008 GenBank mRNA 1 492 . - . ID=MettrDRAFT_0987.t01;Parent=MettrDRAFT_0987
But that doesn't say anything about what those features should be
called (ie, how they should be found when searched for). The same is
true of your "region" (chromosome? plasmid?) lines: they have ID
attributes, but those don't tell GBrowse how to find them. For each
of those region lines, I would add Name attributes that are identical
to the ID attribute, and more importantly, that match the text in the
first column.
I have no idea what is going on with the GBrowse 1.70 instance; are
you using the same GFF? Perhaps fixing it will fix that problem too.
Scott
On Tue, Sep 21, 2010 at 3:31 PM, Grace <gkenney at u.northwestern.edu> wrote:
> Hey -
>
> Thanks for the response. Here're my answers; let me know if there's
> anything else I should send to help.
>
> Generic Genome Browser Version 1.70, with BioPerl etc. up to date
> (since I'd updated pretty much everything in the last few weeks to get
> GBrowse2 going, though I can give details on different modules and so
> on if necessary.) And no, the plugins I am using are BatchDumper,
> FastaDumper, RestrictionAnnotator, FilterTest, and Submitter, so I
> doubt that it is VistaPlot. Furthermore, when none of these other
> plugins are activated, I get identical errors.
>
> Generic Genome Browser version 2.14. The GFF3 file and the genome and
> general GBrowse configuration files are attached. The yeast and
> volvox conf files (not attached) are unchanged from stock except for
> the choice of db_adaptor and db_args, and the addition of the user and
> pass fields for their databases. The conf file for my genome is
> essentially the volvox conf file, with information adapted to fit my
> data (e.g. default features are genes, not the volvox example
> features.)
>
> Thanks!
>
> -Grace
>
> 2010/9/21 Dave Clements, GMOD Help Desk <help at gmod.org>:
>> Hi Grace,
>>
>> I'm CC'ing in the GBrowse list as others may have ideas as well.
>> That's probably the best place to post GBrowse questions.
>>
>> This same Perl error was reported in June 2009. See
>> http://sourceforge.net/mailarchive/forum.php?thread_name=afbd84760906151426hec37eb2i5d9f61262359ef1f%40mail.gmail.com&forum_name=gmod-gbrowse
>>
>> In that case, Cynthia was using the Vista Plot plugin. Are you using
>> that? If so, there is a patch in the thread. If not, we'll have more
>> work to do.
>>
>> What version of GBrowse 1 are you using?
>>
>>
>> For the GBrowse 2 problem, can you send a sample of your GFF? Your
>> conf file might help too.
>>
>> Thanks,
>>
>> Dave C
>>
>> On Mon, Sep 20, 2010 at 11:32 PM, Grace <gkenney at u.northwestern.edu> wrote:
>>> Hi -
>>>
>>> I've got two GBrowse-related questions and I'd appreciate it if you
>>> can point me towards people who can help me troubleshoot them.
>>>
>>> I've been having a problem with uploaded annotation. When I upload
>>> several annotation files to my GBrowse installation, the annotation
>>> tracks display correctly at first, but after looking at a few
>>> genes/etc., all but one of the tracks will stop showing. These errors
>>> show up in my apache logfiles.
>>>
>>> [Sat Sep 18 15:32:55 2010] [error] [client ::1] Use of uninitialized
>>> value $nr_tracks_added in numeric eq (==) at
>>> /opt/local/lib/perl5/site_perl/5.10.1/darwin-multi-2level/Bio/Graphics/Browser.pm
>>> line 1397., referer:
>>> http://localhost/cgi-bin/gbrowse/genome/?name=genename
>>> [Sat Sep 18 15:32:55 2010] [error] [client ::1] Use of uninitialized
>>> value $nr_tracks_added in subtraction (-) at
>>> /opt/local/lib/perl5/site_perl/5.10.1/darwin-multi-2level/Bio/Graphics/Browser.pm
>>> line 1404., referer:
>>> http://localhost/cgi-bin/gbrowse/genome/?name=genename
>>>
>>> This is while running the original GBrowse on OS X 10.6.4; everything
>>> else currently works without problem. Is there anything I can do to
>>> address this?
>>>
>>> I've also got an unrelated bonus question regarding GBrowse2, which
>>> I'm in the process of setting up (using a MySQL backend.) The example
>>> yeast and volvox databases work fine (again, using the MySQL backend);
>>> the genome I am studying does not. Permissions seem to be the same
>>> on conf files, gff3 files, databases, etc. The GFF3 file validates on
>>> the EColiHub validator, and loads fine with bp_seqfeature_load.pl The
>>> MySQL database appears to be correctly populated with the information
>>> imported from the GFF3 file (meaning that with the correct genome
>>> database loaded in MySQL, I can, for example, enter "select * from
>>> sequence;" and get a list of all the sequences/matching IDs from the
>>> sequence table.)
>>>
>>> Looking for any valid landmark results in a "The landmark GeneName was
>>> not found." Only the search panel (containing the "landmark or
>>> region", "examples", and "data source" options") appears; Overview,
>>> Region, and Details all do not appear at all. (The result is the same
>>> as what you would get if you searched for some random invalid phrase
>>> in a working setup (e.g. my yeast or volvox sample databases), but it
>>> occurs even when I search for contig names and gene names/IDs that I
>>> know exist in the GFF3 file/MySQL database.) Nothing untoward shows
>>> up in my MySQL error logs, and there's generally nothing odd in my
>>> Apache logs either except for specific actions like trying to get
>>> chromosome size (n.b. the genome in this case is the default source in
>>> GBrowse.conf):
>>>
>>> [Mon Sep 20 17:08:06 2010] [error] [client ::1] Can't find chromosome
>>> chromname in default database at
>>> /opt/local/lib/perl5/site_perl/5.10.1/darwin-multi-2level/Bio/Graphics/Browser2/DataLoader.pm
>>> line 173., referer:
>>> http://localhost/cgi-bin/gb2/gbrowse/genome/?name=genename
>>>
>>> However, simply trying to load a normal GBrowse page does not produce
>>> any errors, even though no tracks are visible and no landmarks are
>>> found.
>>>
>>> Again, any ideas? I can send logs, gff3 files, conf files, etc. as
>>> necessary. I'd appreciate any help anyone can offer with regards to
>>> either of these problems.
>>> Thanks!
>>>
>>> -Grace
>>>
>>
>>
>>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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