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[Gmod-ajax] Problem with large gff3 files.

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Michael Stoker

[Gmod-ajax] Problem with large gff3 files.

Hi to all,

I have installed jbrowse 1.3 successfully with all the perl modules. I have loaded my fasta files and several tracks from gff3 files which works great.

The problem is as soon as i want to load tracks from larger gff3 files (2GB), the run just ends with a message "killed".

Any idea what i'm doing wrong?

------------------------------------------------------------------------------
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Michael Stoker

[Gmod-ajax] Problem with draw-basepair

Hi again,

I have another problem.

When i run :

bin/draw-basepair-track.pl --gff Models_WoComments_edited.gff --tracklabel BasePairing

I get several outputs like :

working on seq scf7180001244291, bases per pixel 1

Then at the end an error:

Modification of non-creatable array value attempted, subscript -1 at /nfs/http8/strigamia-genome/www/JBrowse-1.3.0-full/bin/../lib/TiledImage/MemoryPrimStorage.pm line 49.

Any idea?

Thanks.

Robert Buels-2

Re: Problem with large gff3 files.

In reply to this post by Michael Stoker

Hi Michael,

Sounds like you ran into the same memory leak bug. Try the 1.3.1
version released today.

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/19/2012 07:01 PM, Michael Stoker wrote:

> Hi to all,
>
> I have installed jbrowse 1.3 successfully with all the perl modules. I
> have loaded my fasta files and several tracks from gff3 files which
> works great.
> The problem is as soon as i want to load tracks from larger gff3 files
> (2GB), the run just ends with a message "killed".
>
> Any idea what i'm doing wrong?
>
>
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Robert Buels-2

Re: Problem with draw-basepair

In reply to this post by Michael Stoker

Could you send me that gff file? Is it OK if I add a part of it to the
JBrowse test suite?

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/19/2012 07:19 PM, Michael Stoker wrote:

> Hi again,
>
> I have another problem.
>
> When i run :
>
> bin/draw-basepair-track.pl --gff Models_WoComments_edited.gff
> --tracklabel BasePairing
>
> I get several outputs like :
> working on seq scf7180001244291, bases per pixel 1
>
> Then at the end an error:
>
> Modification of non-creatable array value attempted, subscript -1 at
> /nfs/http8/strigamia-genome/www/JBrowse-1.3.0-full/bin/../lib/TiledImage/MemoryPrimStorage.pm
> line 49.
>
> Any idea?
>
> Thanks.
>
>
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Michael Stoker

[Gmod-ajax] Another bug.

In reply to this post by Michael Stoker

Hi again,

I have noticed that when i open JBrowse, I have several tracks on the left panel and when i drag them, it just says loading for ages and nothing happens. I have to select another scaffold on the drop down menu then go back to the 1st one so i can see finally the features.

This happens everytime i reload the page.

Also when there are no features, it still says "loading".

What should i do?

Michael Stoker

Re: Another bug.

Sorry forgot to include a screenshot.

Some have no features but it still says "loading".

Any idea how to fix that. Or should i use the new release?

From: Michael Stoker <[hidden email]>
To: "[hidden email]" <[hidden email]>
Sent: Friday, April 20, 2012 10:48 AM
Subject: Another bug.

Hi again,

This happens everytime i reload the page.

Also when there are no features, it still says "loading".

What should i do?

Jbrowse.png (89K) Download Attachment

Robert Buels-2

Re: Problem with large gff3 files.

In reply to this post by Michael Stoker

Does your large blastx.gff file have GFF3 synchronization marks (###) in
it? Without those marks, GFF3 parsers have to parse the entire file in
one chunk, loading is into memory (which takes at least 4x the file size
worth of RAM).

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 08:21 AM, Michael Stoker wrote:

> Hi Robert,
>
> With the new release 1.3.1 , i'm still getting the same error :
>
> $ bin/flatfile-to-json.pl --gff /gff/blastx.gff --tracklabel
> Blastx_protein_match --className feature4 --type protein_match --getType
> --getPhase --getSubs --getLabel --key Blastx_protein_match
> Killed
>
> This file blastx.gff is about 2 GB.
>
> Not sure how i can load the features from this gff file then?
> Do i need another perl module to handle the file size?
> Everything works great for gff files up to 80 MB but not bigger.
>
> ------------------------------------------------------------------------
> *From:* Robert Buels <[hidden email]>
> *To:* Michael Stoker <[hidden email]>
> *Sent:* Friday, April 20, 2012 3:08 AM
> *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
>
> Hi Michael,
>
> Sounds like you ran into the same memory leak bug. Try the 1.3.1
> version released today.
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 04/19/2012 07:01 PM, Michael Stoker wrote:
> > Hi to all,
> >
> > I have installed jbrowse 1.3 successfully with all the perl modules. I
> > have loaded my fasta files and several tracks from gff3 files which
> > works great.
> > The problem is as soon as i want to load tracks from larger gff3 files
> > (2GB), the run just ends with a message "killed".
> >
> > Any idea what i'm doing wrong?
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > For Developers, A Lot Can Happen In A Second.
> > Boundary is the first to Know...and Tell You.
> > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > http://p.sf.net/sfu/Boundary-d2dvs2
> >
> >
> >
> > _______________________________________________
> > Gmod-ajax mailing list
> > [hidden email] <mailto:[hidden email]>
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Robert Buels-2

Re: Another bug.

In reply to this post by Michael Stoker

Those 'loading' tracks definitely have some kind of problem. Is this
JBrowse anywhere online where I can look at it? That's by far the
quickest way to diagnose what its problem is.

If that's not at all an option, do you have any output in your browser's
log? Depending on which browser you are using, this often appears as a
little red icon with an exclamation point in the lower right of your

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 06:01 AM, Michael Stoker wrote:

> Sorry forgot to include a screenshot.
>
> Some have no features but it still says "loading".
>
> Any idea how to fix that. Or should i use the new release?
>
> ------------------------------------------------------------------------
> *From:* Michael Stoker <[hidden email]>
> *To:* "[hidden email]" <[hidden email]>
> *Sent:* Friday, April 20, 2012 10:48 AM
> *Subject:* Another bug.
>
> Hi again,
>
> I have noticed that when i open JBrowse, I have several tracks on the
> left panel and when i drag them, it just says loading for ages and
> nothing happens. I have to select another scaffold on the drop down menu
> then go back to the 1st one so i can see finally the features.
> This happens everytime i reload the page.
> Also when there are no features, it still says "loading".
>
> What should i do?
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Robert Buels-2

Re: Problem with large gff3 files.

In reply to this post by Robert Buels-2

I'd advise either adding the sync marks yourself with something like a
Perl one-liner, or splitting the file up into smaller files (which
accomplishes pretty much the same thing).

If you have contact with the people that generated that file, it would
also be a good idea to point out to them that a GFF3 file that size
without '###' marks is quite difficult to use.

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 08:55 AM, Michael Stoker wrote:

> No it doesn't have, i got the file as it is from the EBI without those
> directives and i'm not even sure how to include those ###. Does this
> mean i can't include features from this gff file then?
>
> ------------------------------------------------------------------------
> *From:* Robert Buels <[hidden email]>
> *To:* Michael Stoker <[hidden email]>;
> "[hidden email]" <[hidden email]>
> *Sent:* Friday, April 20, 2012 1:52 PM
> *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
>
> Does your large blastx.gff file have GFF3 synchronization marks (###) in
> it? Without those marks, GFF3 parsers have to parse the entire file in
> one chunk, loading is into memory (which takes at least 4x the file size
> worth of RAM).
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 04/20/2012 08:21 AM, Michael Stoker wrote:
> > Hi Robert,
> >
> > With the new release 1.3.1 , i'm still getting the same error :
> >
> > $ bin/flatfile-to-json.pl --gff /gff/blastx.gff --tracklabel
> > Blastx_protein_match --className feature4 --type protein_match --getType
> > --getPhase --getSubs --getLabel --key Blastx_protein_match
> > Killed
> >
> > This file blastx.gff is about 2 GB.
> >
> > Not sure how i can load the features from this gff file then?
> > Do i need another perl module to handle the file size?
> > Everything works great for gff files up to 80 MB but not bigger.
> >
> > ------------------------------------------------------------------------
> > *From:* Robert Buels <[hidden email] <mailto:[hidden email]>>
> > *To:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>>
> > *Sent:* Friday, April 20, 2012 3:08 AM
> > *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
> >
> > Hi Michael,
> >
> > Sounds like you ran into the same memory leak bug. Try the 1.3.1
> > version released today.
> >
> > Robert Buels
> > Lead Developer
> > JBrowse - http://jbrowse.org
> >
> > On 04/19/2012 07:01 PM, Michael Stoker wrote:
> > > Hi to all,
> > >
> > > I have installed jbrowse 1.3 successfully with all the perl modules. I
> > > have loaded my fasta files and several tracks from gff3 files which
> > > works great.
> > > The problem is as soon as i want to load tracks from larger gff3 files
> > > (2GB), the run just ends with a message "killed".
> > >
> > > Any idea what i'm doing wrong?
> > >
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > > For Developers, A Lot Can Happen In A Second.
> > > Boundary is the first to Know...and Tell You.
> > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > > http://p.sf.net/sfu/Boundary-d2dvs2
> > >
> > >
> > >
> > > _______________________________________________
> > > Gmod-ajax mailing list
> > > [hidden email]
> <mailto:[hidden email]>
> <mailto:[hidden email]
> <mailto:[hidden email]>>
> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>

Robert Buels-2

Re: Problem with large gff3 files.

Yes, ### before each scaffold would work. A Perl one-liner is a very
small Perl program written entirely on the command line. A Google
search yields a number of different perspectives on it.

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 09:14 AM, Michael Stoker wrote:

> Thanks for the advice, will do and will let them know.
> Should i just add those marks randomly without anything else? Like just
> ### before each scaffold for instance? What do you mean by "Perl on-liner"?
>
> Thanks.
>
> ------------------------------------------------------------------------
> *From:* Robert Buels <[hidden email]>
> *To:* Michael Stoker <[hidden email]>;
> "[hidden email]" <[hidden email]>
> *Sent:* Friday, April 20, 2012 2:02 PM
> *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
>
> I'd advise either adding the sync marks yourself with something like a
> Perl one-liner, or splitting the file up into smaller files (which
> accomplishes pretty much the same thing).
>
> If you have contact with the people that generated that file, it would
> also be a good idea to point out to them that a GFF3 file that size
> without '###' marks is quite difficult to use.
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 04/20/2012 08:55 AM, Michael Stoker wrote:
> > No it doesn't have, i got the file as it is from the EBI without those
> > directives and i'm not even sure how to include those ###. Does this
> > mean i can't include features from this gff file then?
> >
> > ------------------------------------------------------------------------
> > *From:* Robert Buels <[hidden email] <mailto:[hidden email]>>
> > *To:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>>;
> > "[hidden email]
> <mailto:[hidden email]>"
> <[hidden email] <mailto:[hidden email]>>
> > *Sent:* Friday, April 20, 2012 1:52 PM
> > *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
> >
> > Does your large blastx.gff file have GFF3 synchronization marks (###) in
> > it? Without those marks, GFF3 parsers have to parse the entire file in
> > one chunk, loading is into memory (which takes at least 4x the file size
> > worth of RAM).
> >
> > Robert Buels
> > Lead Developer
> > JBrowse - http://jbrowse.org
> >
> > On 04/20/2012 08:21 AM, Michael Stoker wrote:
> > > Hi Robert,
> > >
> > > With the new release 1.3.1 , i'm still getting the same error :
> > >
> > > $ bin/flatfile-to-json.pl --gff /gff/blastx.gff --tracklabel
> > > Blastx_protein_match --className feature4 --type protein_match
> --getType
> > > --getPhase --getSubs --getLabel --key Blastx_protein_match
> > > Killed
> > >
> > > This file blastx.gff is about 2 GB.
> > >
> > > Not sure how i can load the features from this gff file then?
> > > Do i need another perl module to handle the file size?
> > > Everything works great for gff files up to 80 MB but not bigger.
> > >
> > >
> ------------------------------------------------------------------------
> > > *From:* Robert Buels <[hidden email] <mailto:[hidden email]>
> <mailto:[hidden email] <mailto:[hidden email]>>>
> > > *To:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>
> > <mailto:[hidden email]
> <mailto:[hidden email]>>>
> > > *Sent:* Friday, April 20, 2012 3:08 AM
> > > *Subject:* Re: [Gmod-ajax] Problem with large gff3 files.
> > >
> > > Hi Michael,
> > >
> > > Sounds like you ran into the same memory leak bug. Try the 1.3.1
> > > version released today.
> > >
> > > Robert Buels
> > > Lead Developer
> > > JBrowse - http://jbrowse.org
> > >
> > > On 04/19/2012 07:01 PM, Michael Stoker wrote:
> > > > Hi to all,
> > > >
> > > > I have installed jbrowse 1.3 successfully with all the perl
> modules. I
> > > > have loaded my fasta files and several tracks from gff3 files which
> > > > works great.
> > > > The problem is as soon as i want to load tracks from larger gff3
> files
> > > > (2GB), the run just ends with a message "killed".
> > > >
> > > > Any idea what i'm doing wrong?
> > > >
> > > >
> > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > For Developers, A Lot Can Happen In A Second.
> > > > Boundary is the first to Know...and Tell You.
> > > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > > > http://p.sf.net/sfu/Boundary-d2dvs2
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Gmod-ajax mailing list
> > > > [hidden email]
> <mailto:[hidden email]>
> > <mailto:[hidden email]
> <mailto:[hidden email]>>
> > <mailto:[hidden email]
> <mailto:[hidden email]>
> > <mailto:[hidden email]
> <mailto:[hidden email]>>>
> > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> > >
> > >
> >
> >
>
>

Robert Buels-2

Re: Another bug.

In reply to this post by Robert Buels-2

In Google Chrome, Ctrl-Shift-I will bring up the debugging pane, where
you can click the red X icon in the lower right to see the error log.
Could you paste the contents of that in an email?

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 09:07 AM, Michael Stoker wrote:

> Unfortunately the data are private.
> Here are 2 screenshots:
> -the 1st one is how the jbrowse looks like when i open the page
> -the 2nd one is after i selected the 2nd scaffold and then the 1st one
> again. It all loads fine.
>
> Note in the 1st screenshot that in the field text, the scaffold name
> doesn't match the one on the drop down menu. I think that's one of the
> problem.
> But doesn't explain why the scaffolds which have no features still try
> to load something.
>
>
> ------------------------------------------------------------------------
> *From:* Robert Buels <[hidden email]>
> *To:* Michael Stoker <[hidden email]>
> *Cc:* "[hidden email]" <[hidden email]>
> *Sent:* Friday, April 20, 2012 1:59 PM
> *Subject:* Re: [Gmod-ajax] Another bug.
>
> Those 'loading' tracks definitely have some kind of problem. Is this
> JBrowse anywhere online where I can look at it? That's by far the
> quickest way to diagnose what its problem is.
>
> If that's not at all an option, do you have any output in your browser's
> log? Depending on which browser you are using, this often appears as a
> little red icon with an exclamation point in the lower right of your
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 04/20/2012 06:01 AM, Michael Stoker wrote:
> > Sorry forgot to include a screenshot.
> >
> > Some have no features but it still says "loading".
> >
> > Any idea how to fix that. Or should i use the new release?
> >
> > ------------------------------------------------------------------------
> > *From:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>>
> > *To:* "[hidden email]
> <mailto:[hidden email]>"
> <[hidden email] <mailto:[hidden email]>>
> > *Sent:* Friday, April 20, 2012 10:48 AM
> > *Subject:* Another bug.
> >
> > Hi again,
> >
> > I have noticed that when i open JBrowse, I have several tracks on the
> > left panel and when i drag them, it just says loading for ages and
> > nothing happens. I have to select another scaffold on the drop down menu
> > then go back to the 1st one so i can see finally the features.
> > This happens everytime i reload the page.
> > Also when there are no features, it still says "loading".
> >
> > What should i do?
> >
> >
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > For Developers, A Lot Can Happen In A Second.
> > Boundary is the first to Know...and Tell You.
> > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > http://p.sf.net/sfu/Boundary-d2dvs2
> >
> >
> >
> > _______________________________________________
> > Gmod-ajax mailing list
> > [hidden email] <mailto:[hidden email]>
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Michael Stoker

Re: Another bug.

Indeed, it seems like there are many errors:

Failed to load resource: the server responded with a status of 404 (Not Found)

~/JBrowse-1.3.1-full/data/tracks/Maker_CDS/scf7180001235522/trackData.jsonFailed to load resource: the server responded with a status of 404 (Not Found)

~/JBrowse-1.3.1-full/data/tracks/Maker_gene/scf7180001235522/trackData.jsonFailed to load resource: the server responded with a status of 404 (Not Found)

~/JBrowse-1.3.1-full/data/tracks/Maker_exon/scf7180001235522/trackData.jsonFailed to load resource: the server responded with a status of 404 (Not Found)

~/JBrowse-1.3.1-full/data/names/root.jsonFailed to load resource: the server responded with a status of 404 (Not Found)

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_mRNA/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

2dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_CDS/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

2dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_exon/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

2dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_gene/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

2dojo.js:14
Error

dojo.js:14
Error

2dojo.js:14
Error

~/JBrowse-1.3.1-full/data/tracks/Augustus_match/scf7180001235522/trackData.jsonFailed to load resource: the server responded with a status of 404 (Not Found)

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Augustus_match/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

2dojo.js:14
Error

From: Robert Buels <[hidden email]>
To: Michael Stoker <[hidden email]>; "[hidden email]" <[hidden email]>
Sent: Friday, April 20, 2012 3:01 PM
Subject: Re: [Gmod-ajax] Another bug.

Michael Stoker

Re: Another bug.

In reply to this post by Robert Buels-2

This is the errors i get when i first open the jbrowse page:

GET ~/JBrowse-1.3.1-full/data/names/root.json 404 (Not Found)

dojo.js:14
Error

dojo.js:14
Error

dojo.js:14
Error

GET ~/JBrowse-1.3.1-full/data/tracks/Maker_mRNA/scf7180001235522/trackData.json 404 (Not Found)

GET ~/JBrowse-1.3.1-full/data/tracks/Maker_exon/scf7180001235522/trackData.json 404 (Not Found)

GET ~/JBrowse-1.3.1-full/data/tracks/Maker_CDS/scf7180001235522/trackData.json 404 (Not Found)

GET ~/JBrowse-1.3.1-full/data/tracks/Maker_gene/scf7180001235522/trackData.json 404 (Not Found)

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_mRNA/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

dojo.js:14
Error

dojo.js:14
Error

GET ~/JBrowse-1.3.1-full/data/tracks/Augustus_match/scf7180001235522/trackData.json 404 (Not Found)

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_exon/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

dojo.js:14
Error

dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_gene/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

dojo.js:14
Error

dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Maker_CDS/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

dojo.js:14
Error

dojo.js:14
Error

dojo.js:14
Error

jbrowse-min.js:1Error: Unable to load data/tracks/Augustus_match/scf7180001235522/trackData.json status:404

dojo.js:14
TypeError

dojo.js:14
Error

dojo.js:14
Error

From: Robert Buels <[hidden email]>
To: Michael Stoker <[hidden email]>; "[hidden email]" <[hidden email]>
Sent: Friday, April 20, 2012 3:01 PM
Subject: Re: [Gmod-ajax] Another bug.

Michael Stoker

Re: Another bug.

In reply to this post by Robert Buels-2

I think i forgot to run the script generatenames. I'm doing it now and will let you know the results.

From: Robert Buels <[hidden email]>
To: Michael Stoker <[hidden email]>; "[hidden email]" <[hidden email]>
Sent: Friday, April 20, 2012 3:01 PM
Subject: Re: [Gmod-ajax] Another bug.

Michael Stoker

Re: Another bug.

In reply to this post by Robert Buels-2

I think i understand what the problem is.

As i didn't find a way with jbrowse to parse the features according to the source (to get the evidences, this is on the 2nd column on the gff file), i have parsed my final gff and created 8 different smaller gff files corresponding to each evidence.

I have then built tracks for each evidence by running the script on each small gff files that i have produced.

The problem is jbrowse tries to load the trackData.json everytime for each reference sequence for each track even if the specified track doesn't exist for some of those reference sequences.

So when it says "loading" that means there are no tracks for that scaffold.

From: Robert Buels <[hidden email]>
To: Michael Stoker <[hidden email]>; "[hidden email]" <[hidden email]>
Sent: Friday, April 20, 2012 3:01 PM
Subject: Re: [Gmod-ajax] Another bug.

Robert Buels-2

Re: Another bug.

In reply to this post by Michael Stoker

It looks to me like the conjunction of two issues:

1. Some of your scaffolds don't have any data for some of the tracks,
and JBrowse doesn't yet know how to say something intelligent about
that; it just keeps saying 'loading...' when it fails to load. I'll fix
this for 1.4.0, you can track the progress of this issue at
https://github.com/GMOD/jbrowse/issues/108

2. The reference-sequence-selection box might not be updating quite
correctly. This might have something to do with a large number of
reference sequences. Do you have a lot? Say over 100 or so? JBrowse
doesn't do very well with large numbers of reference sequences right
now, which is another thing that is going to be fixed for 1.4.0,
relevant issues for that are:

https://github.com/GMOD/jbrowse/issues/3
https://github.com/GMOD/jbrowse/issues/60 (autocomplete the search box)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 04/20/2012 10:08 AM, Michael Stoker wrote:

> Indeed, it seems like there are many errors:
>
>
> Failed to load resource: the server responded with a status of 404 (Not
> Found)
> ~/JBrowse-1.3.1-full/data/tracks/Maker_CDS/scf7180001235522/trackData.json
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/data/tracks/Maker_CDS/scf7180001235522/trackData.json>Failed
> to load resource: the server responded with a status of 404 (Not Found)
> ~/JBrowse-1.3.1-full/data/tracks/Maker_gene/scf7180001235522/trackData.json
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/data/tracks/Maker_gene/scf7180001235522/trackData.json>Failed
> to load resource: the server responded with a status of 404 (Not Found)
> ~/JBrowse-1.3.1-full/data/tracks/Maker_exon/scf7180001235522/trackData.json
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/data/tracks/Maker_exon/scf7180001235522/trackData.json>Failed
> to load resource: the server responded with a status of 404 (Not Found)
> ~/JBrowse-1.3.1-full/data/names/root.json
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/data/names/root.json>Failed
> to load resource: the server responded with a status of 404 (Not Found)
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> jbrowse-min.js:1
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jbrowse-min.js>Error:
> Unable to load data/tracks/Maker_mRNA/scf7180001235522/trackData.json
> status:404
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> TypeError
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> jbrowse-min.js:1
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jbrowse-min.js>Error:
> Unable to load data/tracks/Maker_CDS/scf7180001235522/trackData.json
> status:404
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> TypeError
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> jbrowse-min.js:1
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jbrowse-min.js>Error:
> Unable to load data/tracks/Maker_exon/scf7180001235522/trackData.json
> status:404
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> TypeError
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> jbrowse-min.js:1
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jbrowse-min.js>Error:
> Unable to load data/tracks/Maker_gene/scf7180001235522/trackData.json
> status:404
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> TypeError
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> ~/JBrowse-1.3.1-full/data/tracks/Augustus_match/scf7180001235522/trackData.json
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/data/tracks/Augustus_match/scf7180001235522/trackData.json>Failed
> to load resource: the server responded with a status of 404 (Not Found)
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
> jbrowse-min.js:1
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jbrowse-min.js>Error:
> Unable to load
> data/tracks/Augustus_match/scf7180001235522/trackData.json status:404
> dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> TypeError
> 2dojo.js:14
> <http://www.strigamia-annotation.org/JBrowse-1.3.1-full/jslib/dojo/dojo.js>
> Error
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
> *
> *
> *
> *
> *From:* Robert Buels <[hidden email]>
> *To:* Michael Stoker <[hidden email]>;
> "[hidden email]" <[hidden email]>
> *Sent:* Friday, April 20, 2012 3:01 PM
> *Subject:* Re: [Gmod-ajax] Another bug.
>
> In Google Chrome, Ctrl-Shift-I will bring up the debugging pane, where
> you can click the red X icon in the lower right to see the error log.
> Could you paste the contents of that in an email?
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 04/20/2012 09:07 AM, Michael Stoker wrote:
> > Unfortunately the data are private.
> > Here are 2 screenshots:
> > -the 1st one is how the jbrowse looks like when i open the page
> > -the 2nd one is after i selected the 2nd scaffold and then the 1st one
> > again. It all loads fine.
> >
> > Note in the 1st screenshot that in the field text, the scaffold name
> > doesn't match the one on the drop down menu. I think that's one of the
> > problem.
> > But doesn't explain why the scaffolds which have no features still try
> > to load something.
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Robert Buels <[hidden email] <mailto:[hidden email]>>
> > *To:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>>
> > *Cc:* "[hidden email]
> <mailto:[hidden email]>"
> <[hidden email] <mailto:[hidden email]>>
> > *Sent:* Friday, April 20, 2012 1:59 PM
> > *Subject:* Re: [Gmod-ajax] Another bug.
> >
> > Those 'loading' tracks definitely have some kind of problem. Is this
> > JBrowse anywhere online where I can look at it? That's by far the
> > quickest way to diagnose what its problem is.
> >
> > If that's not at all an option, do you have any output in your browser's
> > log? Depending on which browser you are using, this often appears as a
> > little red icon with an exclamation point in the lower right of your
> >
> >
> > Robert Buels
> > Lead Developer
> > JBrowse - http://jbrowse.org
> >
> > On 04/20/2012 06:01 AM, Michael Stoker wrote:
> > > Sorry forgot to include a screenshot.
> > >
> > > Some have no features but it still says "loading".
> > >
> > > Any idea how to fix that. Or should i use the new release?
> > >
> > >
> ------------------------------------------------------------------------
> > > *From:* Michael Stoker <[hidden email]
> <mailto:[hidden email]>
> > <mailto:[hidden email]
> <mailto:[hidden email]>>>
> > > *To:* "[hidden email]
> <mailto:[hidden email]>
> > <mailto:[hidden email]
> <mailto:[hidden email]>>"
> > <[hidden email]
> <mailto:[hidden email]>
> <mailto:[hidden email]
> <mailto:[hidden email]>>>
> > > *Sent:* Friday, April 20, 2012 10:48 AM
> > > *Subject:* Another bug.
> > >
> > > Hi again,
> > >
> > > I have noticed that when i open JBrowse, I have several tracks on the
> > > left panel and when i drag them, it just says loading for ages and
> > > nothing happens. I have to select another scaffold on the drop down
> menu
> > > then go back to the 1st one so i can see finally the features.
> > > This happens everytime i reload the page.
> > > Also when there are no features, it still says "loading".
> > >
> > > What should i do?
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > > For Developers, A Lot Can Happen In A Second.
> > > Boundary is the first to Know...and Tell You.
> > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > > http://p.sf.net/sfu/Boundary-d2dvs2
> > >
> > >
> > >
> > > _______________________________________________
> > > Gmod-ajax mailing list
> > > [hidden email]
> <mailto:[hidden email]>
> <mailto:[hidden email]
> <mailto:[hidden email]>>
> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>
>
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax