Tracks won't render

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Tracks won't render

Scooter Willis-2
Tracks won't render
In the process of adding in updated gff3 files and editing the conf the tracks will no longer render. Looking in the apache2 error log I get the following error message. I am running gbrowse2 should be the latest install.

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



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Re: Tracks won't render

Lincoln Stein
Hi Scooter,

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

Lincoln

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

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: Tracks won't render

Scooter Willis-2
In reply to this post by Scooter Willis-2
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----
From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 11:52 am
Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>

Hi Scooter,

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

Lincoln

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

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
[hidden email]
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Re: Tracks won't render

Lincoln Stein
Hi Scooter,

Sorry, I misunderstood your problem. I would suggest removing all the GFF3 files except for the one that contains the chromosome names and lengths, then adding them back one-by-one until the problem reappears.

I have had the same problem with modperl processes not exiting properly, which is one reason that I prefer FastCGI. You can kill the mod_perl processes without a reboot by doing a "killall -9 apache2".

Lincoln 

On Mon, Jun 21, 2010 at 12:16 PM, Scooter Willis <[hidden email]> wrote:
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----

From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 11:52 am

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Hi Scooter,

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

Lincoln

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

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




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



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
[hidden email]
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Re: Tracks won't render

Scooter Willis-2
In reply to this post by Scooter Willis-2
Lincoln

I have tried removing gff3 files and can not get it to render. I also created a new setup and only included the fasta file and same error message. Adding a gff3 file didn't change anything.

What is the expected behavior if you just have a fasta file?

Does any filebin the designated database dir get loaded?

What happens when you remove a file?

Do you typically kill apache to force a reload after changes? Mainly concerned with removing items that are no longer in the gff3 file.

I will try and clone yeast basic and see if the problem continues.

Thanks

Scooter

----- Reply message -----
From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 12:29 pm
Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>

Hi Scooter,

Sorry, I misunderstood your problem. I would suggest removing all the GFF3 files except for the one that contains the chromosome names and lengths, then adding them back one-by-one until the problem reappears.

I have had the same problem with modperl processes not exiting properly, which is one reason that I prefer FastCGI. You can kill the mod_perl processes without a reboot by doing a "killall -9 apache2".

Lincoln 

On Mon, Jun 21, 2010 at 12:16 PM, Scooter Willis <[hidden email]> wrote:
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----

From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 11:52 am

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Hi Scooter,

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

Lincoln

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

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




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



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
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Re: Tracks won't render

Lincoln Stein
Hi Scooter,

If you are using mod_perl, then changing the GFF3 files won't have any effect until you restart the server. At a minimum, to get a display, you need a single GFF3 file that contains the chromosome names and their coordinates in the following format:

Chr1 . chromosome 1 15982944 . . . Name=Chr1

Lincoln

On Mon, Jun 21, 2010 at 12:50 PM, Scooter Willis <[hidden email]> wrote:
Lincoln

I have tried removing gff3 files and can not get it to render. I also created a new setup and only included the fasta file and same error message. Adding a gff3 file didn't change anything.

What is the expected behavior if you just have a fasta file?

Does any filebin the designated database dir get loaded?

What happens when you remove a file?

Do you typically kill apache to force a reload after changes? Mainly concerned with removing items that are no longer in the gff3 file.

I will try and clone yeast basic and see if the problem continues.

Thanks

Scooter

----- Reply message -----
From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 12:29 pm

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>

Hi Scooter,

Sorry, I misunderstood your problem. I would suggest removing all the GFF3 files except for the one that contains the chromosome names and lengths, then adding them back one-by-one until the problem reappears.

I have had the same problem with modperl processes not exiting properly, which is one reason that I prefer FastCGI. You can kill the mod_perl processes without a reboot by doing a "killall -9 apache2".

Lincoln 

On Mon, Jun 21, 2010 at 12:16 PM, Scooter Willis <[hidden email]> wrote:
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----

From: "Lincoln Stein" <[hidden email]>
Date: Mon, Jun 21, 2010 11:52 am

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <[hidden email]>
Hi Scooter,

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

Lincoln

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

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



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



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



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: Tracks won't render

Scooter Willis-2
Re: [GMOD-devel] Tracks won't render Lincoln

The FastCGI would return an Internal Server Error on different occasions and the reason I was using mod_perl. Running with gb2 or mgb2 option in the url would work as expected. Currently same behavior FastCGI gives Internal Server Error but gb2 and mgb2 will render the page currently with the track not being shown. Not sure if this provides any additional clues as to the overall problem. What is strange is that what worked before with minimal problems has stopped working.

I am going to try and get the volvox example working.

Scooter

[Mon Jun 21 13:25:40 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2661)
[Mon Jun 21 13:25:41 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2662)
[Mon Jun 21 13:25:43 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2663)
[Mon Jun 21 13:25:44 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2664)
[Mon Jun 21 13:25:46 2010] [warn] FastCGI: scheduled the start of the last (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" process: reached dynamicMaxClassProcs (10)
[Mon Jun 21 13:25:46 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2665)
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] RUN(): POST: http://dyadic-c1-server/fgb2/gbrowse/c1/ prefix=1_;action=autocomplete;_= at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] add_user_tracks() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] testing for asynchronous event() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] asynchronous exit at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] RUN(): POST: http://dyadic-c1-server/fgb2/gbrowse/c1/ prefix=1_g;action=autocomplete;_= at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] add_user_tracks() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] testing for asynchronous event() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] asynchronous exit at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: comm with (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" aborted: (first read) idle timeout (30 sec), referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: incomplete headers (0 bytes) received from server "/usr/lib/cgi-bin/gb2/gbrowse", referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:12 2010] [error] [client 10.10.250.4] File does not exist: /var/www/favicon.ico
[Mon Jun 21 13:26:18 2010] [notice] GBrowse FastCGI process caught sigPIPE. Exiting... (pid 2658)
[Mon Jun 21 13:26:18 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" (pid 2658) terminated by calling exit with status '0'



On 6/21/10 12:54 PM, "Lincoln Stein" <lincoln.stein@...> wrote:

Hi Scooter,

If you are using mod_perl, then changing the GFF3 files won't have any effect until you restart the server. At a minimum, to get a display, you need a single GFF3 file that contains the chromosome names and their coordinates in the following format:

Chr1 . chromosome 1 15982944 . . . Name=Chr1

Lincoln

On Mon, Jun 21, 2010 at 12:50 PM, Scooter Willis <HWillis@...> wrote:
Lincoln

I have tried removing gff3 files and can not get it to render. I also created a new setup and only included the fasta file and same error message. Adding a gff3 file didn't change anything.

What is the expected behavior if you just have a fasta file?

Does any filebin the designated database dir get loaded?

What happens when you remove a file?

Do you typically kill apache to force a reload after changes? Mainly concerned with removing items that are no longer in the gff3 file.

I will try and clone yeast basic and see if the problem continues.

Thanks

Scooter

----- Reply message -----
From: "Lincoln Stein" <lincoln.stein@...>
Date: Mon, Jun 21, 2010 12:29 pm

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <HWillis@...>
Cc: "gmod-devel@..." <gmod-devel@...>

Hi Scooter,

Sorry, I misunderstood your problem. I would suggest removing all the GFF3 files except for the one that contains the chromosome names and lengths, then adding them back one-by-one until the problem reappears.

I have had the same problem with modperl processes not exiting properly, which is one reason that I prefer FastCGI. You can kill the mod_perl processes without a reboot by doing a "killall -9 apache2".

Lincoln 

On Mon, Jun 21, 2010 at 12:16 PM, Scooter Willis <HWillis@...> wrote:
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----

From: "Lincoln Stein" <lincoln.stein@...>
Date: Mon, Jun 21, 2010 11:52 am

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <HWillis@...>

Cc: "gmod-devel@..." <gmod-devel@...>

Hi Scooter,

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

Lincoln

On Sun, Jun 20, 2010 at 11:30 PM, Scooter Willis <HWillis@...> wrote:

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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Re: Tracks won't render

Lincoln Stein
You could try stepping back to an earlier version of GBrowse2. It may be that the most recent version contains a subtle bug.

Is the log file that you attached from the time of an Internal Server Error when running under FastCGI? FastCGI seems very stable here.

Lincoln

On Mon, Jun 21, 2010 at 1:34 PM, Scooter Willis <[hidden email]> wrote:
Lincoln

The FastCGI would return an Internal Server Error on different occasions and the reason I was using mod_perl. Running with gb2 or mgb2 option in the url would work as expected. Currently same behavior FastCGI gives Internal Server Error but gb2 and mgb2 will render the page currently with the track not being shown. Not sure if this provides any additional clues as to the overall problem. What is strange is that what worked before with minimal problems has stopped working.

I am going to try and get the volvox example working.

Scooter

[Mon Jun 21 13:25:40 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2661)
[Mon Jun 21 13:25:41 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2662)
[Mon Jun 21 13:25:43 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2663)
[Mon Jun 21 13:25:44 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2664)
[Mon Jun 21 13:25:46 2010] [warn] FastCGI: scheduled the start of the last (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" process: reached dynamicMaxClassProcs (10)
[Mon Jun 21 13:25:46 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" started (pid 2665)
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] RUN(): POST: http://dyadic-c1-server/fgb2/gbrowse/c1/ prefix=1_;action=autocomplete;_= at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] add_user_tracks() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] testing for asynchronous event() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:25:51 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2656] asynchronous exit at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] RUN(): POST: http://dyadic-c1-server/fgb2/gbrowse/c1/ prefix=1_g;action=autocomplete;_= at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 180., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] add_user_tracks() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 187., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] testing for asynchronous event() at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 198., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:04 2010] [error] [client 10.10.250.4] FastCGI: server "/usr/lib/cgi-bin/gb2/gbrowse" stderr: [2657] asynchronous exit at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 200., referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: comm with (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" aborted: (first read) idle timeout (30 sec), referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: incomplete headers (0 bytes) received from server "/usr/lib/cgi-bin/gb2/gbrowse", referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:12 2010] [error] [client 10.10.250.4] File does not exist: /var/www/favicon.ico
[Mon Jun 21 13:26:18 2010] [notice] GBrowse FastCGI process caught sigPIPE. Exiting... (pid 2658)
[Mon Jun 21 13:26:18 2010] [warn] FastCGI: (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" (pid 2658) terminated by calling exit with status '0'




On 6/21/10 12:54 PM, "Lincoln Stein" <lincoln.stein@...> wrote:

Hi Scooter,

If you are using mod_perl, then changing the GFF3 files won't have any effect until you restart the server. At a minimum, to get a display, you need a single GFF3 file that contains the chromosome names and their coordinates in the following format:

Chr1 . chromosome 1 15982944 . . . Name=Chr1

Lincoln

On Mon, Jun 21, 2010 at 12:50 PM, Scooter Willis <HWillis@...> wrote:
Lincoln

I have tried removing gff3 files and can not get it to render. I also created a new setup and only included the fasta file and same error message. Adding a gff3 file didn't change anything.

What is the expected behavior if you just have a fasta file?

Does any filebin the designated database dir get loaded?

What happens when you remove a file?

Do you typically kill apache to force a reload after changes? Mainly concerned with removing items that are no longer in the gff3 file.

I will try and clone yeast basic and see if the problem continues.

Thanks

Scooter

----- Reply message -----
From: "Lincoln Stein" <lincoln.stein@...>
Date: Mon, Jun 21, 2010 12:29 pm

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <HWillis@...>
Cc: "gmod-devel@..." <gmod-devel@...>

Hi Scooter,

Sorry, I misunderstood your problem. I would suggest removing all the GFF3 files except for the one that contains the chromosome names and lengths, then adding them back one-by-one until the problem reappears.

I have had the same problem with modperl processes not exiting properly, which is one reason that I prefer FastCGI. You can kill the mod_perl processes without a reboot by doing a "killall -9 apache2".

Lincoln 

On Mon, Jun 21, 2010 at 12:16 PM, Scooter Willis <HWillis@...> wrote:
I am loading everything into memory so not sure how that impacts tracking down the problem. I could never figure out how to issue an apache restart because the mod perl keeps running and locks port 80. When I try and kill process that own port 80 after a stop they would respawn. So I have been rebooting to force a reload of changes. Not sure if this could impact anything.

I will try and create a new conf setup using yeast basic and see if it also has a problem.

Thanks

Scooter

----- Reply message -----

From: "Lincoln Stein" <lincoln.stein@...>
Date: Mon, Jun 21, 2010 11:52 am

Subject: [GMOD-devel] Tracks won't render
To: "Scooter Willis" <HWillis@...>

Cc: "gmod-devel@..." <gmod-devel@...>

Hi Scooter,

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

Lincoln

On Sun, Jun 20, 2010 at 11:30 PM, Scooter Willis <HWillis@...> wrote:

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

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

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

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

Thanks

Scooter

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

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

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

# size of the region
region segment         = 10000

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

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

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

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

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

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


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

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

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


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

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



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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
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Re: Tracks won't render

Scooter Willis-2
Re: [GMOD-devel] Tracks won't render Lincoln

I thought this was indicating an error on the idle timeout.

How do I find out what version is currently running. The browser says 2.0. I did the install about a month ago.

I know it is something simple as it was working fairly well.

Scooter


On 6/21/10 1:44 PM, "Lincoln Stein" <lincoln.stein@...> wrote:

[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: comm with (dynamic) server "/usr/lib/cgi-bin/gb2/gbrowse" aborted: (first read) idle timeout (30 sec), referer: http://dyadic-c1-server/fgb2/gbrowse/c1/
[Mon Jun 21 13:26:11 2010] [error] [client 10.10.250.4] FastCGI: incomplete headers (0 bytes) received from server "/usr/lib/cgi-bin/gb2/gbrowse", referer: http://dyadic-c1-server/fgb2/gbrowse/c1/

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