Tracks wont render..

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Tracks wont render..

Jayaraman, Pushkala
I get the exact same error as Scooter mentioned.. my older databases
work..
But my new ones don't..
The error is also in the same line line 708 in Render.pm.


The in-memory databases work though..

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu

Message: 1
Date: Sun, 20 Jun 2010 23:30:00 -0400
From: Scooter Willis <[hidden email]>
Subject: [GMOD-devel] Tracks won't render
To: "[hidden email]"
        <[hidden email]>
Message-ID: <C84454F8.4499%[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"


In the process of adding in updated gff3 files and editing the conf the
tracks will no longer render. Looking in the apache2 error log I get the
following error message. I am running gbrowse2 should be the latest
install.

    Use of uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 708.

I looked at the source and not being familiar with code not sure how to
track down the problem. I turned on debugging but didn't see any
additional error messages. I have tried to put everything back but for
some reason I am missing the obvious. I have included the conf file in
the event I am missing the obvious.

Any thoughts, I have tried changing almost everything back to the basic
setup and can't get the error message to change? The yeast demos work as
expected and I only get the above error message when loading my
database.

Thanks

Scooter

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
        -dir /var/www/gbrowse2/databases/c1scaffold

# just the basic track dumper plugin
plugins     = FilterTest RestrictionAnnotator TrackDumper FastaDumper

# list of tracks to turn on by default
default tracks = GlimmerPredictions

# size of the region
region segment         = 10000

# examples to show in the introduction
examples = scaffold00016
           GH10
           PF00734

# feature to show on startup
initial landmark = scaffold00016:51000..54999

########################
# Default glyph settings
########################

[TRACK DEFAULTS]
glyph         = generic
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
# where to link to when user clicks in detailed view
link          = AUTO

################## TRACK CONFIGURATION ####################
# the remainder of the sections configure individual tracks
###########################################################

[GlimmerPredictions]
feature      = mRNA:GlimmerHMM
glyph        = gene
stranded     = 1
bgcolor      = blue
height       = 10
key          = Glimmer Predicted genes


[GeneMarkPredictions]
feature      = gene:GeneMark.hmm
glyph        = gene
stranded     = 1
bgcolor      = red
height       = 10
key          = GeneMark Predicted genes

[GeneMarkUniprotHits]
feature      = match:GeneMark.hmm_UNIPROT
glyph        = span
height       = 5
bgcolor      = red
key          = GeneMark Uniprot Hits
link         = http://www.uniprot.com/uniprot/$Alias
link_target  = _blank

[GeneidPredictions]
feature      = gene:geneid_v1.3
glyph        = gene
stranded     = 1
bgcolor      = green
height       = 10
key          = Geneid Predicted genes


[DNA]
glyph          = dna
global feature = 1
height         = 40
do_gc          = 1
gc_window      = auto
fgcolor        = red
axis_color     = blue
strand         = both
category       = DNA
key            = DNA/GC Content

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 6frame
category       = DNA
key            = 6-frame translation


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Message: 2
Date: Mon, 21 Jun 2010 11:38:16 -0400
From: Scooter Willis <[hidden email]>
Subject: [GMOD-devel] Tracks wont render and search does not work
        Gbrowse 2.0
To: "[hidden email]"
        <[hidden email]>
Message-ID: <C844FFA8.44C1%[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"


I really need some guidance as I have tried everything to figure out why
my gbrowse2 setup stop working for my config. The pre-installed configs
work as expected.

I created a new conf with just the basics and only the fasta data and it
appears I get the same error which appears to be related to my problem
of not rendering the tracks. The fasta file is unchanged and was working
before I started updating gff3 files with more data.

I am getting the following error message "Use of initialized valie in
concatenation" but I have no clue how to track down what is causing it.



Mon Jun 21 11:29:15 2010] [error] [client 10.10.250.4] File does not
exist: /var/www/favicon.ico
[1950] RUN(): POST: http://dyadic-c1-server/gb2/gbrowse/yeast/ source=c1
at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1951] RUN(): GET: http://dyadic-c1-server/gb2/gbrowse/c1/ source=c1 at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1951] add_user_tracks() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187.
[1951] testing for asynchronous event() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198.
[1951] init() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 205.
[1951] update_state() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 208.
[1951] render() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 215.
[1951] cleanup at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 219.
[1951] session flush at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 223.
[1951] synchronous exit at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 225.
[Mon Jun 21 11:29:38 2010] [error] [client 10.10.250.4] File does not
exist: /var/www/favicon.ico
[1953] RUN(): POST: http://dyadic-c1-server/gb2/gbrowse/c1/
prefix=1_;action=autocomplete;_= at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1953] add_user_tracks() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187.
[1953] testing for asynchronous event() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198.
[1953] asynchronous exit at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200.
[1955] RUN(): POST: http://dyadic-c1-server/gb2/gbrowse/c1/
force_submit=0;plugin_find=0;name=1_g;Search=Search at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1955] add_user_tracks() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187.
[1955] testing for asynchronous event() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198.
[1955] init() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 205.
[1955] update_state() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 208.
[1955] render() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 215.
Use of uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 708.
[1955] cleanup at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 219.
[1955] session flush at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 223.
[1955] synchronous exit at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 225.
[1954] RUN(): POST: http://dyadic-c1-server/gb2/gbrowse/c1/
prefix=1_g;action=autocomplete;_= at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1954] add_user_tracks() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187.
[1954] testing for asynchronous event() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198.
[Mon Jun 21 11:30:14 2010] [error] [client 10.10.250.4] File does not
exist: /var/www/favicon.ico
[1954] asynchronous exit at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200.
[1957] RUN(): POST: http://dyadic-c1-server/gb2/gbrowse/c1/
action=add_tracks;track_names=GeneMarkPredictions;_= at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180.
[1957] add_user_tracks() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187.
[1957] testing for asynchronous event() at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198.
[1957] asynchronous exit at
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200.


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Message: 3
Date: Mon, 21 Jun 2010 11:52:00 -0400
From: Lincoln Stein <[hidden email]>
Subject: Re: [GMOD-devel] Tracks won't render
To: Scooter Willis <[hidden email]>
Cc: "[hidden email]"
        <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="windows-1252"

Hi Scooter,

Is there any chance that you've wiped out the chromosomal scaffolds?
Could
you check your database to confirm that the chromosomes are still there?

Lincoln

On Sun, Jun 20, 2010 at 11:30 PM, Scooter Willis
<[hidden email]>wrote:

>
> In the process of adding in updated gff3 files and editing the conf
the
> tracks will no longer render. Looking in the apache2 error log I get
the
> following error message. I am running gbrowse2 should be the latest
install.
>
>     Use of uninitialized value in concatenation (.) or string at
> /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 708.
>
> I looked at the source and not being familiar with code not sure how
to
> track down the problem. I turned on debugging but didn?t see any
additional
> error messages. I have tried to put everything back but for some
reason I am
> missing the obvious. I have included the conf file in the event I am
missing
> the obvious.
>
> Any thoughts, I have tried changing almost everything back to the
basic
> setup and can?t get the error message to change? The yeast demos work
as
> expected and I only get the above error message when loading my
database.

>
> Thanks
>
> Scooter
>
> [GENERAL]
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor memory
>         -dir /var/www/gbrowse2/databases/c1scaffold
>
> # just the basic track dumper plugin
> plugins     = FilterTest RestrictionAnnotator TrackDumper FastaDumper
>
> # list of tracks to turn on by default
> default tracks = GlimmerPredictions
>
> # size of the region
> region segment         = 10000
>
> # examples to show in the introduction
> examples = scaffold00016
>            GH10
>            PF00734
>
> # feature to show on startup
> initial landmark = scaffold00016:51000..54999
>
> ########################
> # Default glyph settings
> ########################
>
> [TRACK DEFAULTS]
> glyph         = generic
> height        = 10
> bgcolor       = lightgrey
> fgcolor       = black
> font2color    = blue
> label density = 25
> bump density  = 100
> # where to link to when user clicks in detailed view
> link          = AUTO
>
> ################## TRACK CONFIGURATION ####################
> # the remainder of the sections configure individual tracks
> ###########################################################
>
> [GlimmerPredictions]
> feature      = mRNA:GlimmerHMM
> glyph        = gene
> stranded     = 1
> bgcolor      = blue
> height       = 10
> key          = Glimmer Predicted genes
>
>
> [GeneMarkPredictions]
> feature      = gene:GeneMark.hmm
> glyph        = gene
> stranded     = 1
> bgcolor      = red
> height       = 10
> key          = GeneMark Predicted genes
>
> [GeneMarkUniprotHits]
> feature      = match:GeneMark.hmm_UNIPROT
> glyph        = span
> height       = 5
> bgcolor      = red
> key          = GeneMark Uniprot Hits
> link         = http://www.uniprot.com/uniprot/$Alias
> link_target  = _blank
>
> [GeneidPredictions]
> feature      = gene:geneid_v1.3
> glyph        = gene
> stranded     = 1
> bgcolor      = green
> height       = 10
> key          = Geneid Predicted genes
>
>
> [DNA]
> glyph          = dna
> global feature = 1
> height         = 40
> do_gc          = 1
> gc_window      = auto
> fgcolor        = red
> axis_color     = blue
> strand         = both
> category       = DNA
> key            = DNA/GC Content
>
> [Translation]
> glyph          = translation
> global feature = 1
> height         = 40
> fgcolor        = purple
> start_codons   = 0
> stop_codons    = 1
> translation    = 6frame
> category       = DNA
> key            = 6-frame translation
>
>
>
>
>
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------

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>
>


--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
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