Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm

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Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm

JINGJING JIN-2
Dear all,

I try to add a new database to the GBrowse.

I have added the conf file in GBrowse.conf:

[oilpalm]
description  = oilpalm database
path         = oilpalm.conf

Then, I have build a oilpalm.conf with very simple configuration:
[GENERAL]
description   = oilpalm chromosome
database      = annotations

initial landmark = p5_sc00196:1,128,977..1,302,826

balloon tips    = 1
aggregators =
plugins = Aligner RestrictionAnnotator TrackDumper


# where to link to when user clicks in detailed view
link          = AUTO
#link_target   = _blank

# what image widths to offer
#image widths  = 450 640 800 1024 1280

# category table configuration

# size of the region
region segment         = 15000

autocomplete = 1

default tracks = Locus
                         ProteinCoding
                 GC:region

# The class of the feature that is used as the reference for all others
# "Sequence" is the default - change it if you use something else
reference class = Sequence

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000
500000 1000000

overview units = M
# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources   = 1

# colors of the overview, detailed map and key
overview bgcolor = whitesmoke
detailed bgcolor = aliceblue
#key bgcolor      = lightsteelblue

# examples to show in the introduction
examples = augustus_masked-p5_sc00196-processed-gene-0.1
           =snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1
      ABC11_171G2
           AtMRP11
           p5_sc00196:1,128,977..1,302,826
         


# "automatic" classes to try when an unqualified identifier is given
automatic classes = contig gene

#################################
# database definitions
#################################

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                    -dsn     oilpalm
                -user    nobody
search options = exact, -fulltext, +autocomplete


[TOOLTIPS]
intro = sub {
                my $args  = shift;
                my $feat  = $args->{feature};
                my $name  = $feat->display_name;
                my $type  = $feat->primary_tag;
                my $class = $feat->class;
                my $source = $feat->source;
                my $extra = join(' ',$feat->each_tag_value('Note')) if
$feat->has_tag('Note');
                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';
                my $msg   = "Hello, I am $name, a$n $type from $source";
               # $msg     .= "<br>I am described as a /*$extra*/" if $extra;
               # $msg     .= "<br>Click to see the sequence of $name";
                return "
$name
" .
                       "
$msg
";
           }
full_sequence = sub {
                  my $args = shift;
                  my $feat = $args->{feature};
                  my $name  = $feat->display_name;
                  my $seq = $feat->seq->seq;
                  $seq =~ s/(\S{75})/$1\n/g;
                  return "<pre style='font-size:8pt'>>$name\n$seq</pre>";
               }



# Default glyph settings
[TRACK DEFAULTS]
glyph         = generic
database      = annotations
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

[GC:region]
glyph        = dna
global feature = 1
height       = 40
gc_window    = auto
do_gc        = 1
strand       = both
fgcolor      = red
axis_color   = blue
show summary  = 0   # no summary of this one
key          = GC Content


[Locus]
feature       = gene:maker
glyph         = generic
bgcolor       = darksalmon
fgcolor       = black
font2color   = blue
strand_arrow = 1
height       = 6
ignore_sub_part = pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA
snRNA rRNA lincRNA Pre-miRNA NAT
description   = 1
key           = Locus
category     = Gene
title           = sub {
                    my $feature = shift;
                    my $n = $feature->name();
                    my $ref = $feature->seq_id();
                    my $start = $feature->start();
                    my $end = $feature->end();
                    return "Locus: $n $ref:$start..$end";
                }
citation     = Each locus along with its type is shown here.  Loci are
essentially equivalent to genes.


[ProteinCoding]
feature         = mRNA:maker
glyph           = processed_transcript
bgcolor         = steelblue
fgcolor         = blue
utr_color       = lightblue
label density   = 50
label           = sub {
                    my $feature = shift;
                    my $n = $feature->name();
                    my ($alias) = $feature->attributes('Note');
                    if ($alias ne ""){
                        $alias =~ s/%2C/,/g;
                        return "$n ($alias)";
                    } else {
                        return $n;
                    }
                }
bump density    = 150
description     = sub {
                        my $feature = shift;
                        my ($conf) = $feature->attributes('Conf');
                        if ($conf ne ""){
                                return "Confidence : " . $conf;
                        }
                }
key             = Protein Coding Gene
category        = Gene

[CDS]
feature       = CDS:maker
glyph         = cds
height = 30
sixframe = 1
ignore_empty_phase = 1
frame0f       = cadetblue
frame1f       = blue
frame2f       = darkblue
frame0r       = darkred
frame1r       = red
frame2r       = crimson
font2color = blue
description = 0
category = Gene
key           = CDS


At the same time, I have added the oilpalm database and related data to
mysql.

However, when I try to visualize it, the display is like this: Can't call
method "new" on an undefined value

I have searched the error log of apache:

[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for GENERAL]description   = oilpalm chromosomedb_adaptor    =
Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t          
-dsn     oilpalm                -user    nobodyinitial landmark =
p5_sc00196:1,128,977..1,302,826plugins \t= Aligner RestrictionAnnotator
TrackDumper# where to link to when user clicks in detailed viewlink        
= AUTO#link_target   = _blank# what image widths to offer#image widths  =
450 640 800 1024 1280# category table configuration# size of the
regionregion segment         = 15000autocomplete = 1default tracks =
Locus\t\t         ProteinCoding                 GC:region# The class of the
feature that is used as the reference for all others# "Sequence" is the
default - change it if you use something elsereference class = Sequence# max
and default segment sizes for detailed viewmax segment     = 500000default
segment = 50000# zoom levelszoom levels    = 50 100 200 1000 2000 5000 10000
20000 40000 100000 200000 500000 1000000overview units = M# whether to show
the sources popup menu (0=false, 1=true; defaults to true)show sources   =
1# colors of the overview, detailed map and keyoverview bgcolor =
whitesmokedetailed bgcolor = aliceblue#key bgcolor      = lightsteelblue#
examples to show in the introductionexamples =
augustus_masked-p5_sc00196-processed-gene-0.1          
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t  
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t [TOOLTIPS]intro = sub {              
my $args  = shift;                my $feat  = $args->{feature};              
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;              
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');              
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericheight        = 10bgcolor      
= lightgreyfgcolor       = blackfont2color    = bluelabel density = 25bump
density  = 100# where to link to when user clicks in detailed viewlink        
= AUTO### TRACK CONFIGURATION ##### the remainder of the sections configure
individual tracks[GC:region]glyph        = dnaglobal feature = 1height      
= 40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey        
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory    
\t= Genetitle           = sub {                    my $feature = shift;                  
my $n = $feature->name();                    my $ref = $feature->seq_id();                  
my $start = $feature->start();                    my $end = $feature->end();                  
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {                  
my $feature = shift;                    my $n = $feature->name();                  
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){                      
$alias =~ s/%2C/,/g;                        return "$n ($alias)";                  
} else {                        return $n;                    }              
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){                              
return "Confidence : " . $conf;                        }                }key            
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44


For this problem, I have searched for previous posting and according to
their suggestions: add warn "track = $track"; in the
Bio/Graphics/Browser2/DataSource.pm;

The the message in error log of apache change to:

Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
GENERAL]description   = oilpalm chromosomedatabase      = annotationsinitial
landmark = p5_sc00196:1,128,977..1,302,826balloon tips    = 1aggregators \t=
plugins \t= Aligner RestrictionAnnotator TrackDumper# where to link to when
user clicks in detailed viewlink          = AUTO#link_target   = _blank#
what image widths to offer#image widths  = 450 640 800 1024 1280# category
table configuration# size of the regionregion segment         =
15000autocomplete = 1default tracks = Locus\t\t         ProteinCoding                
GC:region# The class of the feature that is used as the reference for all
others# "Sequence" is the default - change it if you use something
elsereference class = Sequence# max and default segment sizes for detailed
viewmax segment     = 500000default segment = 50000# zoom levelszoom levels  
= 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000
1000000overview units = M# whether to show the sources popup menu (0=false,
1=true; defaults to true)show sources   = 1# colors of the overview,
detailed map and keyoverview bgcolor = whitesmokedetailed bgcolor =
aliceblue#key bgcolor      = lightsteelblue# examples to show in the
introductionexamples = augustus_masked-p5_sc00196-processed-gene-0.1          
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t  
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t # "automatic" classes to try
when an unqualified identifier is givenautomatic classes = contig gene
################################## database
definitions#################################[annotations:database]db_adaptor  
= Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t          
-dsn     oilpalm                -user    nobody[TOOLTIPS]intro = sub {              
my $args  = shift;                my $feat  = $args->{feature};              
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;              
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');              
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericdatabase      =
annotationsheight        = 10bgcolor       = lightgreyfgcolor       =
blackfont2color    = bluelabel density = 25bump density  = 100# where to
link to when user clicks in detailed viewlink          = AUTO### TRACK
CONFIGURATION ##### the remainder of the sections configure individual
tracks[GC:region]glyph        = dnaglobal feature = 1height       =
40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey        
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory    
\t= Genetitle           = sub {                    my $feature = shift;                  
my $n = $feature->name();                    my $ref = $feature->seq_id();                  
my $start = $feature->start();                    my $end = $feature->end();                  
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {                  
my $feature = shift;                    my $n = $feature->name();                  
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){                      
$alias =~ s/%2C/,/g;                        return "$n ($alias)";                  
} else {                        return $n;                    }              
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){                              
return "Confidence : " . $conf;                        }                }key            
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for GENERAL]description   = oilpalm chromosomedatabase      =
annotationsinitial landmark = p5_sc00196:1,128,977..1,302,826balloon tips  
= 1aggregators \t= plugins \t= Aligner RestrictionAnnotator TrackDumper#
where to link to when user clicks in detailed viewlink          =
AUTO#link_target   = _blank# what image widths to offer#image widths  = 450
640 800 1024 1280# category table configuration# size of the regionregion
segment         = 15000autocomplete = 1default tracks = Locus\t\t        
ProteinCoding                 GC:region# The class of the feature that is
used as the reference for all others# "Sequence" is the default - change it
if you use something elsereference class = Sequence# max and default segment
sizes for detailed viewmax segment     = 500000default segment = 50000# zoom
levelszoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000overview units = M# whether to show the sources popup
menu (0=false, 1=true; defaults to true)show sources   = 1# colors of the
overview, detailed map and keyoverview bgcolor = whitesmokedetailed bgcolor
= aliceblue#key bgcolor      = lightsteelblue# examples to show in the
introductionexamples = augustus_masked-p5_sc00196-processed-gene-0.1          
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t  
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t # "automatic" classes to try
when an unqualified identifier is givenautomatic classes = contig gene
################################## database
definitions#################################[annotations:database]db_adaptor  
= Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t          
-dsn     oilpalm                -user    nobody[TOOLTIPS]intro = sub {              
my $args  = shift;                my $feat  = $args->{feature};              
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;              
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');              
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericdatabase      =
annotationsheight        = 10bgcolor       = lightgreyfgcolor       =
blackfont2color    = bluelabel density = 25bump density  = 100# where to
link to when user clicks in detailed viewlink          = AUTO### TRACK
CONFIGURATION ##### the remainder of the sections configure individual
tracks[GC:region]glyph        = dnaglobal feature = 1height       =
40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey        
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory    
\t= Genetitle           = sub {                    my $feature = shift;                  
my $n = $feature->name();                    my $ref = $feature->seq_id();                  
my $start = $feature->start();                    my $end = $feature->end();                  
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {                  
my $feature = shift;                    my $n = $feature->name();                  
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){                      
$alias =~ s/%2C/,/g;                        return "$n ($alias)";                  
} else {                        return $n;                    }              
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){                              
return "Confidence : " . $conf;                        }                }key            
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.



However, I am still not sure where is wrong for my config.

Can anyone give me some suggestions?

Thanks!

jingjing







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Re: Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm

Scott Cain
Hi Jingjing,

There is almost certainly a syntax error in one of your config files, but it is not very easy to read config files pasted into email.  Can you reply to the list with your GBrowse.conf and data source conf files attached?

In the mean time, you may also want to try simplifying your data source conf--removing callbacks and unnecessary directives, which may help you identify where the syntax error is.

Thanks,
Scott



On Thu, Feb 6, 2014 at 1:07 AM, jjjscuedu <[hidden email]> wrote:
Dear all,

I try to add a new database to the GBrowse.

I have added the conf file in GBrowse.conf:

[oilpalm]
description  = oilpalm database
path         = oilpalm.conf

Then, I have build a oilpalm.conf with very simple configuration:
[GENERAL]
description   = oilpalm chromosome
database      = annotations

initial landmark = p5_sc00196:1,128,977..1,302,826

balloon tips    = 1
aggregators     =
plugins         = Aligner RestrictionAnnotator TrackDumper


# where to link to when user clicks in detailed view
link          = AUTO
#link_target   = _blank

# what image widths to offer
#image widths  = 450 640 800 1024 1280

# category table configuration

# size of the region
region segment         = 15000

autocomplete = 1

default tracks = Locus
                         ProteinCoding
                 GC:region

# The class of the feature that is used as the reference for all others
# "Sequence" is the default - change it if you use something else
reference class = Sequence

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000
500000 1000000

overview units = M
# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources   = 1

# colors of the overview, detailed map and key
overview bgcolor = whitesmoke
detailed bgcolor = aliceblue
#key bgcolor      = lightsteelblue

# examples to show in the introduction
examples = augustus_masked-p5_sc00196-processed-gene-0.1
           =snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1
           ABC11_171G2
           AtMRP11
           p5_sc00196:1,128,977..1,302,826



# "automatic" classes to try when an unqualified identifier is given
automatic classes = contig gene

#################################
# database definitions
#################################

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                    -dsn     oilpalm
                -user    nobody
search options = exact, -fulltext, +autocomplete


[TOOLTIPS]
intro = sub {
                my $args  = shift;
                my $feat  = $args->{feature};
                my $name  = $feat->display_name;
                my $type  = $feat->primary_tag;
                my $class = $feat->class;
                my $source = $feat->source;
                my $extra = join(' ',$feat->each_tag_value('Note')) if
$feat->has_tag('Note');
                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';
                my $msg   = "Hello, I am $name, a$n $type from $source";
               # $msg     .= "<br>I am described as a /*$extra*/" if $extra;
               # $msg     .= "<br>Click to see the sequence of $name";
                return "
$name
" .
                       "
$msg
";
           }
full_sequence = sub {
                  my $args = shift;
                  my $feat = $args->{feature};
                  my $name  = $feat->display_name;
                  my $seq = $feat->seq->seq;
                  $seq =~ s/(\S{75})/$1\n/g;
                  return "<pre style='font-size:8pt'>>$name\n$seq</pre>";
               }



# Default glyph settings
[TRACK DEFAULTS]
glyph         = generic
database      = annotations
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

[GC:region]
glyph        = dna
global feature = 1
height       = 40
gc_window    = auto
do_gc        = 1
strand       = both
fgcolor      = red
axis_color   = blue
show summary  = 0   # no summary of this one
key          = GC Content


[Locus]
feature         = gene:maker
glyph           = generic
bgcolor         = darksalmon
fgcolor         = black
font2color      = blue
strand_arrow    = 1
height          = 6
ignore_sub_part = pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA
snRNA rRNA lincRNA Pre-miRNA NAT
description     = 1
key             = Locus
category        = Gene
title           = sub {
                    my $feature = shift;
                    my $n = $feature->name();
                    my $ref = $feature->seq_id();
                    my $start = $feature->start();
                    my $end = $feature->end();
                    return "Locus: $n $ref:$start..$end";
                }
citation        = Each locus along with its type is shown here.  Loci are
essentially equivalent to genes.


[ProteinCoding]
feature         = mRNA:maker
glyph           = processed_transcript
bgcolor         = steelblue
fgcolor         = blue
utr_color       = lightblue
label density   = 50
label           = sub {
                    my $feature = shift;
                    my $n = $feature->name();
                    my ($alias) = $feature->attributes('Note');
                    if ($alias ne ""){
                        $alias =~ s/%2C/,/g;
                        return "$n ($alias)";
                    } else {
                        return $n;
                    }
                }
bump density    = 150
description     = sub {
                        my $feature = shift;
                        my ($conf) = $feature->attributes('Conf');
                        if ($conf ne ""){
                                return "Confidence : " . $conf;
                        }
                }
key             = Protein Coding Gene
category        = Gene

[CDS]
feature         = CDS:maker
glyph           = cds
height          = 30
sixframe        = 1
ignore_empty_phase      = 1
frame0f         = cadetblue
frame1f         = blue
frame2f         = darkblue
frame0r         = darkred
frame1r         = red
frame2r         = crimson
font2color      = blue
description     = 0
category        = Gene
key             = CDS


At the same time, I have added the oilpalm database and related data to
mysql.

However, when I try to visualize it, the display is like this: Can't call
method "new" on an undefined value

I have searched the error log of apache:

[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for GENERAL]description   = oilpalm chromosomedb_adaptor    =
Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t
-dsn     oilpalm                -user    nobodyinitial landmark =
p5_sc00196:1,128,977..1,302,826plugins \t= Aligner RestrictionAnnotator
TrackDumper# where to link to when user clicks in detailed viewlink
= AUTO#link_target   = _blank# what image widths to offer#image widths  =
450 640 800 1024 1280# category table configuration# size of the
regionregion segment         = 15000autocomplete = 1default tracks =
Locus\t\t         ProteinCoding                 GC:region# The class of the
feature that is used as the reference for all others# "Sequence" is the
default - change it if you use something elsereference class = Sequence# max
and default segment sizes for detailed viewmax segment     = 500000default
segment = 50000# zoom levelszoom levels    = 50 100 200 1000 2000 5000 10000
20000 40000 100000 200000 500000 1000000overview units = M# whether to show
the sources popup menu (0=false, 1=true; defaults to true)show sources   =
1# colors of the overview, detailed map and keyoverview bgcolor =
whitesmokedetailed bgcolor = aliceblue#key bgcolor      = lightsteelblue#
examples to show in the introductionexamples =
augustus_masked-p5_sc00196-processed-gene-0.1
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t [TOOLTIPS]intro = sub {
my $args  = shift;                my $feat  = $args->{feature};
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericheight        = 10bgcolor
= lightgreyfgcolor       = blackfont2color    = bluelabel density = 25bump
density  = 100# where to link to when user clicks in detailed viewlink
= AUTO### TRACK CONFIGURATION ##### the remainder of the sections configure
individual tracks[GC:region]glyph        = dnaglobal feature = 1height
= 40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory
\t= Genetitle           = sub {                    my $feature = shift;
my $n = $feature->name();                    my $ref = $feature->seq_id();
my $start = $feature->start();                    my $end = $feature->end();
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {
my $feature = shift;                    my $n = $feature->name();
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){
$alias =~ s/%2C/,/g;                        return "$n ($alias)";
} else {                        return $n;                    }
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){
return "Confidence : " . $conf;                        }                }key
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 937.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 943.
[Thu Feb 06 16:49:36 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44


For this problem, I have searched for previous posting and according to
their suggestions: add warn "track = $track"; in the
Bio/Graphics/Browser2/DataSource.pm;

The the message in error log of apache change to:

Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
GENERAL]description   = oilpalm chromosomedatabase      = annotationsinitial
landmark = p5_sc00196:1,128,977..1,302,826balloon tips    = 1aggregators \t=
plugins \t= Aligner RestrictionAnnotator TrackDumper# where to link to when
user clicks in detailed viewlink          = AUTO#link_target   = _blank#
what image widths to offer#image widths  = 450 640 800 1024 1280# category
table configuration# size of the regionregion segment         =
15000autocomplete = 1default tracks = Locus\t\t         ProteinCoding
GC:region# The class of the feature that is used as the reference for all
others# "Sequence" is the default - change it if you use something
elsereference class = Sequence# max and default segment sizes for detailed
viewmax segment     = 500000default segment = 50000# zoom levelszoom levels
= 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000
1000000overview units = M# whether to show the sources popup menu (0=false,
1=true; defaults to true)show sources   = 1# colors of the overview,
detailed map and keyoverview bgcolor = whitesmokedetailed bgcolor =
aliceblue#key bgcolor      = lightsteelblue# examples to show in the
introductionexamples = augustus_masked-p5_sc00196-processed-gene-0.1
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t # "automatic" classes to try
when an unqualified identifier is givenautomatic classes = contig gene
################################## database
definitions#################################[annotations:database]db_adaptor
= Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t
-dsn     oilpalm                -user    nobody[TOOLTIPS]intro = sub {
my $args  = shift;                my $feat  = $args->{feature};
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericdatabase      =
annotationsheight        = 10bgcolor       = lightgreyfgcolor       =
blackfont2color    = bluelabel density = 25bump density  = 100# where to
link to when user clicks in detailed viewlink          = AUTO### TRACK
CONFIGURATION ##### the remainder of the sections configure individual
tracks[GC:region]glyph        = dnaglobal feature = 1height       =
40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory
\t= Genetitle           = sub {                    my $feature = shift;
my $n = $feature->name();                    my $ref = $feature->seq_id();
my $start = $feature->start();                    my $end = $feature->end();
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {
my $feature = shift;                    my $n = $feature->name();
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){
$alias =~ s/%2C/,/g;                        return "$n ($alias)";
} else {                        return $n;                    }
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){
return "Confidence : " . $conf;                        }                }key
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for GENERAL]description   = oilpalm chromosomedatabase      =
annotationsinitial landmark = p5_sc00196:1,128,977..1,302,826balloon tips
= 1aggregators \t= plugins \t= Aligner RestrictionAnnotator TrackDumper#
where to link to when user clicks in detailed viewlink          =
AUTO#link_target   = _blank# what image widths to offer#image widths  = 450
640 800 1024 1280# category table configuration# size of the regionregion
segment         = 15000autocomplete = 1default tracks = Locus\t\t
ProteinCoding                 GC:region# The class of the feature that is
used as the reference for all others# "Sequence" is the default - change it
if you use something elsereference class = Sequence# max and default segment
sizes for detailed viewmax segment     = 500000default segment = 50000# zoom
levelszoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000overview units = M# whether to show the sources popup
menu (0=false, 1=true; defaults to true)show sources   = 1# colors of the
overview, detailed map and keyoverview bgcolor = whitesmokedetailed bgcolor
= aliceblue#key bgcolor      = lightsteelblue# examples to show in the
introductionexamples = augustus_masked-p5_sc00196-processed-gene-0.1
=snap_masked-p5_sc00196-processed-gene-0.2-mRNA-1    \t   ABC11_171G2\t\t
AtMRP11\t   p5_sc00196:1,128,977..1,302,826\t # "automatic" classes to try
when an unqualified identifier is givenautomatic classes = contig gene
################################## database
definitions#################################[annotations:database]db_adaptor
= Bio::DB::SeqFeature::Storedb_args       = -adaptor DBI::mysql\t
-dsn     oilpalm                -user    nobody[TOOLTIPS]intro = sub {
my $args  = shift;                my $feat  = $args->{feature};
my $name  = $feat->display_name;                my $type  =
$feat->primary_tag;                my $class = $feat->class;
my $source = $feat->source;                my $extra = join('
',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';                my $msg   =
"Hello, I am $name, a$n $type from $source";               # $msg     .=
"<br>I am described as a /*$extra*/" if $extra;               # $msg     .=
"<br>Click to see the sequence of $name";                return "
$name
" .                       "
$msg
";           }full_sequence = sub {\t          my $args = shift;\t\t  my
$feat = $args->{feature};\t\t  my $name  = $feat->display_name;\t\t  my $seq
= $feat->seq->seq;\t\t  $seq =~ s/(\\S{75})/$1\\n/g;\t\t  return "<pre
style='font-size:8pt'>>$name\\n$seq</pre>";               }# Default glyph
settings[TRACK DEFAULTS]glyph         = genericdatabase      =
annotationsheight        = 10bgcolor       = lightgreyfgcolor       =
blackfont2color    = bluelabel density = 25bump density  = 100# where to
link to when user clicks in detailed viewlink          = AUTO### TRACK
CONFIGURATION ##### the remainder of the sections configure individual
tracks[GC:region]glyph        = dnaglobal feature = 1height       =
40gc_window    = autodo_gc        = 1strand       = bothfgcolor      =
redaxis_color   = blueshow summary  = 0   # no summary of this onekey
= GC Content[Locus]feature      \t= gene:makerglyph        \t=
genericbgcolor      \t= darksalmonfgcolor      \t= blackfont2color   \t=
bluestrand_arrow \t= 1height       \t= 6ignore_sub_part =
pseudogenic_transcript mRNA mRNA_TE_gene ncRNA tRNA snoRNA snRNA rRNA
lincRNA Pre-miRNA NATdescription  \t= 1key          \t= Locuscategory
\t= Genetitle           = sub {                    my $feature = shift;
my $n = $feature->name();                    my $ref = $feature->seq_id();
my $start = $feature->start();                    my $end = $feature->end();
return "Locus: $n $ref:$start..$end";                }citation     \t= Each
locus along with its type is shown here.  Loci are essentially equivalent to
genes.[ProteinCoding]feature         = mRNA:makerglyph           =
processed_transcriptbgcolor         = steelbluefgcolor         =
blueutr_color       = lightbluelabel density   = 50label           = sub {
my $feature = shift;                    my $n = $feature->name();
my ($alias) = $feature->attributes('Note');\t\t    if ($alias ne ""){
$alias =~ s/%2C/,/g;                        return "$n ($alias)";
} else {                        return $n;                    }
}bump density    = 150description     = sub {                        my
$feature = shift;                        my ($conf) =
$feature->attributes('Conf');                        if ($conf ne ""){
return "Confidence : " . $conf;                        }                }key
= Protein Coding Gene category        = Gene[CDS at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Thu Feb 06 16:58:01 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.



However, I am still not sure where is wrong for my config.

Can anyone give me some suggestions?

Thanks!

jingjing







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Re: Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm

JINGJING JIN-2
Dear Scott,

Thanks for your kindly reply.

I have simplify the config file for my data. However, the error was still
there:

[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $dbid in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] track = general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Unknown database
defined for general at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $db in hash element at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 1065.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value in concatenation (.) or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] track =
plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 927.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Use of
uninitialized value $symbolic_db_name in join or string at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 939.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Unknown database
defined for plugin:RestrictionAnnotator at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataSource.pm line 945.
[Sat Feb 08 14:31:20 2014] [error] [client 10.50.70.161] Could not open
database: Can't call method "new" on an undefined value at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataBase.pm line 44.

The below is the configure file:




oilpalm.txt
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712175/oilpalm.txt>  

GBrowse.txt
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712175/GBrowse.txt>  



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