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gbrowse configuration help

Irina Garanina
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







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Re: gbrowse configuration help

Scott Cain
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: gbrowse configuration help

Scott Cain
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: gbrowse configuration help

Irina Garanina
Scott, 

if I trying to navigate to another section of the genome I get another error Can't call method "get_feature_by_name" on an undefined value

I found apache log only:

[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value in concatenation (.) or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

2016-09-12 18:30 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: gbrowse configuration help

Scott Cain
Ah, I see, you have a line that looks like this:

database      = mycoplasma

which means that there should be a database defined in the config with the name "mycoplasma", but the databases defined look like this:

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

where one of those should be like "[mycoplasma:database]" and in fact, since they are the same thing, you only need one.  In the example config, there are two because it demonstrates that you can have more than one database configured, but you don't need to.  Just be sure to change any references in track configurations to use the database named "mycoplasma" instead of annotations or scaffolds.

Scott


On Mon, Sep 12, 2016 at 12:05 PM, Irina Garanina <[hidden email]> wrote:
Scott, 

if I trying to navigate to another section of the genome I get another error Can't call method "get_feature_by_name" on an undefined value

I found apache log only:

[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value in concatenation (.) or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

2016-09-12 18:30 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: gbrowse configuration help

Scott Cain
Hi Irina,

Please keep the GBrowse mailing list cc'ed on your replies (ie, "reply all").

Any time you make a change to the configuration file, be sure to use the "update appearance" button, and if you're using fastcgi, be sure to restart apache first too.

Another suggestion is that you take the example configuration and make changes very incrementally, like only changing the name of the database and making sure it still works, and then changing the name of the GFF file (without changing the contents), and then changing the contents of the GFF file, etc.  That way you'll be able to tell what is causing the problem when it comes up.

Scott


On Mon, Sep 12, 2016 at 12:24 PM, Irina Garanina <[hidden email]> wrote:
It can be some problem with database name

but I think I have another problem in logs, I changed database name and deleted the second annotation database and error in log did not changed   

2016-09-12 19:12 GMT+03:00 Scott Cain <[hidden email]>:
Ah, I see, you have a line that looks like this:

database      = mycoplasma

which means that there should be a database defined in the config with the name "mycoplasma", but the databases defined look like this:

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

where one of those should be like "[mycoplasma:database]" and in fact, since they are the same thing, you only need one.  In the example config, there are two because it demonstrates that you can have more than one database configured, but you don't need to.  Just be sure to change any references in track configurations to use the database named "mycoplasma" instead of annotations or scaffolds.

Scott


On Mon, Sep 12, 2016 at 12:05 PM, Irina Garanina <[hidden email]> wrote:
Scott, 

if I trying to navigate to another section of the genome I get another error Can't call method "get_feature_by_name" on an undefined value

I found apache log only:

[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value in concatenation (.) or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

2016-09-12 18:30 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: gbrowse configuration help

Irina Garanina
Sorry, Scott, for cc

I tried to make changes incrementally: if I used text from volvox.conf without changes in file mycoplasma.conf and volvox data, respectively, it still did not worked, worked only in case I used volvox.conf itself in GBbrowse.conf like:

[mycoplasma]
description = Mycoplasma gallisepticum
path        = volvox.conf

also do not work if I changed the name of directory with gff3 file

if I change file volvox.conf like this, it works, but I can't see the tracks and can't navigate:

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir  /data5/bio/gbrowse2/mycoplasma



2016-09-12 20:09 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed on your replies (ie, "reply all").

Any time you make a change to the configuration file, be sure to use the "update appearance" button, and if you're using fastcgi, be sure to restart apache first too.

Another suggestion is that you take the example configuration and make changes very incrementally, like only changing the name of the database and making sure it still works, and then changing the name of the GFF file (without changing the contents), and then changing the contents of the GFF file, etc.  That way you'll be able to tell what is causing the problem when it comes up.

Scott


On Mon, Sep 12, 2016 at 12:24 PM, Irina Garanina <[hidden email]> wrote:
It can be some problem with database name

but I think I have another problem in logs, I changed database name and deleted the second annotation database and error in log did not changed   

2016-09-12 19:12 GMT+03:00 Scott Cain <[hidden email]>:
Ah, I see, you have a line that looks like this:

database      = mycoplasma

which means that there should be a database defined in the config with the name "mycoplasma", but the databases defined look like this:

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

where one of those should be like "[mycoplasma:database]" and in fact, since they are the same thing, you only need one.  In the example config, there are two because it demonstrates that you can have more than one database configured, but you don't need to.  Just be sure to change any references in track configurations to use the database named "mycoplasma" instead of annotations or scaffolds.

Scott


On Mon, Sep 12, 2016 at 12:05 PM, Irina Garanina <[hidden email]> wrote:
Scott, 

if I trying to navigate to another section of the genome I get another error Can't call method "get_feature_by_name" on an undefined value

I found apache log only:

[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value in concatenation (.) or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

2016-09-12 18:30 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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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Re: gbrowse configuration help

Scott Cain
And when you make that change (changing the path and file name for the database), what is the error in the error log?  This is why you make small, incremental changes, so that when things go wrong, you can isolate what happened and know from the error message what to do.  My guess is that there is an error in the log about file or directory permissions.

Scott


On Tue, Sep 13, 2016 at 9:11 AM, Irina Garanina <[hidden email]> wrote:
Sorry, Scott, for cc

I tried to make changes incrementally: if I used text from volvox.conf without changes in file mycoplasma.conf and volvox data, respectively, it still did not worked, worked only in case I used volvox.conf itself in GBbrowse.conf like:

[mycoplasma]
description = Mycoplasma gallisepticum
path        = volvox.conf

also do not work if I changed the name of directory with gff3 file

if I change file volvox.conf like this, it works, but I can't see the tracks and can't navigate:

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir  /data5/bio/gbrowse2/mycoplasma



2016-09-12 20:09 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed on your replies (ie, "reply all").

Any time you make a change to the configuration file, be sure to use the "update appearance" button, and if you're using fastcgi, be sure to restart apache first too.

Another suggestion is that you take the example configuration and make changes very incrementally, like only changing the name of the database and making sure it still works, and then changing the name of the GFF file (without changing the contents), and then changing the contents of the GFF file, etc.  That way you'll be able to tell what is causing the problem when it comes up.

Scott


On Mon, Sep 12, 2016 at 12:24 PM, Irina Garanina <[hidden email]> wrote:
It can be some problem with database name

but I think I have another problem in logs, I changed database name and deleted the second annotation database and error in log did not changed   

2016-09-12 19:12 GMT+03:00 Scott Cain <[hidden email]>:
Ah, I see, you have a line that looks like this:

database      = mycoplasma

which means that there should be a database defined in the config with the name "mycoplasma", but the databases defined look like this:

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

where one of those should be like "[mycoplasma:database]" and in fact, since they are the same thing, you only need one.  In the example config, there are two because it demonstrates that you can have more than one database configured, but you don't need to.  Just be sure to change any references in track configurations to use the database named "mycoplasma" instead of annotations or scaffolds.

Scott


On Mon, Sep 12, 2016 at 12:05 PM, Irina Garanina <[hidden email]> wrote:
Scott, 

if I trying to navigate to another section of the genome I get another error Can't call method "get_feature_by_name" on an undefined value

I found apache log only:

[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $dbid in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for general at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $db in hash element at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1063.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value in concatenation (.) or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 183.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Use of uninitialized value $symbolic_db_name in join or string at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 937.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Unknown database defined for plugin:RestrictionAnnotator at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 943.
[Mon Sep 12 19:04:15 2016] [error] [client 10.210.28.43] Could not open database: Can't call method "new" on an undefined value at /srv/common/lib/perl5/site_perl/5.16.1//x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44.

2016-09-12 18:30 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

Please keep the GBrowse mailing list cc'ed in your replies.

Most likely what you're seeing is a result of caching in the web browser.  Follow the Preferences link, hit the "Update appearance", and then try navigating to another section of the genome.  If you still see that message, look at the apache error log to see what error message it is giving, and if that is not helpful to you, send it to the list and we'll take a look.

Scott


On Mon, Sep 12, 2016 at 11:07 AM, Irina Garanina <[hidden email]> wrote:
Scott,

thank you for your answer

I corrected gff3 file to:

chr      GI      chromosome      1       985433  .       .       .       Name=chr
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I still see the same error 

Irina


2016-09-12 17:54 GMT+03:00 Scott Cain <[hidden email]>:
Hi Irina,

The problem is here:

chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

The line where you specify the "reference sequence" (that is, the thing where your features are located) needs to have the same name in column 1 as you declare in column 9, so it should look like this instead:

CP006916.3      GI      chromosome      1       985433  .       .       .       Name=CP006916.3

and the other lines in the GFF file should have the same thing in column 1 (assume there is only one chromosome).

Scott

On Mon, Sep 12, 2016 at 10:29 AM, Irina Garanina <[hidden email]> wrote:
Dear somebody,

I tried to create my own database, but I have an error Can't call method "new" on an undefined value

I tested my browser in volvox and yeast databases and it worked well

For my database I created conf file mycoplasma.conf:

[GENERAL]
description   = mycoplasma
database      = mycoplasma

initial landmark = chr:1..1800

# bring in the special Submitter plugin for the rubber-band select menu
plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter
autocomplete = 1

default tracks = Genes

# examples to show in the introduction
examples = chr

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

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

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /data5/bio/gbrowse2/mycoplasma
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

[Genes]
feature      = gene
glyph        = segments
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise


Then in directory /data5/bio/gbrowse2/mycoplasma I created standard fasta file with my chromosome mycoplasma.fasta:

>chr
seq...

and gff3 file mycoplasma.gff3:

##gff-version 3

# file: mycoplasma.gff3
chr      GI      chromosome      1       985433  .       .       .       Name=CP006916.3
chr      GI      gene    1891    2680    .       +       .       Name=parA
chr      GI      gene    3160    4546    .       +       .       Name=dnaA

and I added strings in the end of GBrowse.conf file:

[mycoplasma]
description = Mycoplasma gallisepticum S6
path        = mycoplasma.conf


Please, help me


Dr. Garanina
Laboratory of proteomics
FRCC PCM, Moscow, Russia







------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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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