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From: Lankerovich, M. <Mic...@sw...> - 2012-05-23 19:15:33
|
Small change in test.wig file:
test.wig
variableStep chrom=chrY span=114
24659973 12
variableStep chrom=chrY span=85
24660123 12
________________________________
From: Lankerovich, Michael [Mic...@sw...]
Sent: Wednesday, May 23, 2012 10:53 AM
To: Michael Stoker; gmo...@li...
Subject: [Gmod-ajax] wig-to-json.pl bug?
Here is a simple test wig file to demonstrate a problem. I am using jbrowse-1.2.
test.wig
variableStep chrom=chrY span=114
24659973 2
variableStep chrom=chrY span=85
24660123 12
perl bin/wig-to-json.pl --key "Test" --tracklabel "Test" --wig test.wig
The output should look like this:
---------------------------------
| |
--------------------------------------------- ---------------------------------
But it looks like this:
----------------------------------
| |
--------- ----------------------------------
I think the reason is because it combines 2 PNG files and the border is right here:
|
|
24660000
Is any way to fix it?
Thank you.
Michael Lankerovich
|
|
From: Lankerovich, M. <Mic...@sw...> - 2012-05-23 17:53:12
|
Here is a simple test wig file to demonstrate a problem. I am using jbrowse-1.2.
test.wig
variableStep chrom=chrY span=114
24659973 2
variableStep chrom=chrY span=85
24660123 12
perl bin/wig-to-json.pl --key "Test" --tracklabel "Test" --wig test.wig
The output should look like this:
---------------------------------
| |
--------------------------------------------- ---------------------------------
But it looks like this:
----------------------------------
| |
--------- ----------------------------------
I think the reason is because it combines 2 PNG files and the border is right here:
|
|
24660000
Is any way to fix it?
Thank you.
Michael Lankerovich
|
|
From: MLSC <mls...@gm...> - 2012-05-17 05:59:35
|
Hi Robert, Thanks for the reply. Yes, I had firfox version 6. now I have installed version 12. It works fine with 12th version. thanks again. Regards, MLSC On Thu, May 17, 2012 at 12:59 AM, Robert Buels <rb...@gm...> wrote: > Also, if this Firefox is older than Firefox 10, it may not work. We > don't support Firefox older than 10. > > Robert Buels > Lead Developer > JBrowse - http://jbrowse.org > > On 05/16/2012 07:37 AM, MLSC wrote: > > Hello friends, > > > > I have installed JBrowse in my linux system. when I try to open link in > > firefox it does not work at all. I find just a gray color line with > > "Jbrowse Bookmark help" links in firefox. But it works fine with > > Internet explorer. Hence may I know what is going wrong with firefox? > > Any suggestions will be helpfull. > > > > Thanking you in anticipation. > > > > Regards, > > mlsc > > > > > > > > > ------------------------------------------------------------------------------ > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > > > > > _______________________________________________ > > Gmod-ajax mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Robert B. <rb...@gm...> - 2012-05-16 21:59:40
|
Also, if this Firefox is older than Firefox 10, it may not work. We don't support Firefox older than 10. Robert Buels Lead Developer JBrowse - http://jbrowse.org On 05/16/2012 07:37 AM, MLSC wrote: > Hello friends, > > I have installed JBrowse in my linux system. when I try to open link in > firefox it does not work at all. I find just a gray color line with > "Jbrowse Bookmark help" links in firefox. But it works fine with > Internet explorer. Hence may I know what is going wrong with firefox? > Any suggestions will be helpfull. > > Thanking you in anticipation. > > Regards, > mlsc > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
|
From: Raymond W. <rw...@cu...> - 2012-05-16 15:14:12
|
Hi mlsc, Quoting MLSC <mls...@gm...>: > I have installed JBrowse in my linux system. when I try to open link in > firefox it does not work at all. I find just a gray color line with > "Jbrowse Bookmark help" links in firefox. But it works fine with Internet > explorer. Hence may I know what is going wrong with firefox? Any > suggestions will be helpfull. I've had no problems with Firefox and also installed JBrowse on a Linux system. Some things you might want to consider: * What version of Firefox are you using? * Can you view the JBrowse site demonstration sites listed here: http://jbrowse.org/demos/ without any problems? A long shot might be to see if any extensions you've added to Firefox that might be causing you problems. I doubt this, though. Also, as you browse your site with Firefox and IE, take a look at the server's error and access logs and see if there is any thing different between the two. Ray ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk |
|
From: MLSC <mls...@gm...> - 2012-05-16 11:37:27
|
Hello friends, I have installed JBrowse in my linux system. when I try to open link in firefox it does not work at all. I find just a gray color line with "Jbrowse Bookmark help" links in firefox. But it works fine with Internet explorer. Hence may I know what is going wrong with firefox? Any suggestions will be helpfull. Thanking you in anticipation. Regards, mlsc |
|
From: Scott C. <sc...@sc...> - 2012-05-04 15:28:36
|
Hello,
As we are trying to plan for next years GMOD meeting, we would like to
decide between two venues as soon as possible. To help us decide,
we've put together a simple survey. We are asking your help in
deciding between:
* San Diego, California in January before or after the Plant and
Animal Genomes meeting
* Cambridge, England in April before or after the International
Society of Biocurators meeting.
Each option has its upsides: the Plant and Animal Genomes is a large
meeting attended by several members of the GMOD community, so it would
likely have a fairly high attendance. On the other hand, having a
meeting in Cambridge would make it easier for European members of the
GMOD community to attend. Please share your thoughts with us and take
this survey.
http://www.surveymonkey.com/s/CPC25P5
Thanks,
Scott
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
|
|
From: Robert B. <rb...@gm...> - 2012-04-20 14:33:55
|
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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...>; > "gmo...@li..." <gmo...@li...> > *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 <rb...@gm... <mailto:rb...@gm...>> > > *To:* Michael Stoker <mic...@ro... > <mailto:mic...@ro...>> > > *Cc:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 <mic...@ro... > <mailto:mic...@ro...> > > <mailto:mic...@ro... > <mailto:mic...@ro...>>> > > > *To:* "gmo...@li... > <mailto:gmo...@li...> > > <mailto:gmo...@li... > <mailto:gmo...@li...>>" > > <gmo...@li... > <mailto:gmo...@li...> > <mailto:gmo...@li... > <mailto:gmo...@li...>>> > > > *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 > > > Gmo...@li... > <mailto:Gmo...@li...> > <mailto:Gmo...@li... > <mailto:Gmo...@li...>> > > > 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 > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Michael S. <mic...@ro...> - 2012-04-20 14:31:50
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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 <rb...@gm...> To: Michael Stoker <mic...@ro...>; "gmo...@li..." <gmo...@li...> 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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *Cc:* "gmo...@li..." <gmo...@li...> > *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 <mic...@ro... > <mailto:mic...@ro...>> > > *To:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Michael S. <mic...@ro...> - 2012-04-20 14:14:52
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I think i forgot to run the script generatenames. I'm doing it now and will let you know the results. ________________________________ From: Robert Buels <rb...@gm...> To: Michael Stoker <mic...@ro...>; "gmo...@li..." <gmo...@li...> 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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *Cc:* "gmo...@li..." <gmo...@li...> > *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 <mic...@ro... > <mailto:mic...@ro...>> > > *To:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Michael S. <mic...@ro...> - 2012-04-20 14:12:51
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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:14Error dojo.js:14Error dojo.js:14Error 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:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_mRNA/scf7180001235522/trackData.json status:404 dojo.js:14TypeError dojo.js:14Error dojo.js:14Error GET ~/JBrowse-1.3.1-full/data/tracks/Augustus_match/scf7180001235522/trackData.json 404 (Not Found) dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_exon/scf7180001235522/trackData.json status:404 dojo.js:14TypeError dojo.js:14Error dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_gene/scf7180001235522/trackData.json status:404 dojo.js:14TypeError dojo.js:14Error dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_CDS/scf7180001235522/trackData.json status:404 dojo.js:14TypeError dojo.js:14Error dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Augustus_match/scf7180001235522/trackData.json status:404 dojo.js:14TypeError dojo.js:14Error dojo.js:14Error ________________________________ From: Robert Buels <rb...@gm...> To: Michael Stoker <mic...@ro...>; "gmo...@li..." <gmo...@li...> 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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *Cc:* "gmo...@li..." <gmo...@li...> > *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 <mic...@ro... > <mailto:mic...@ro...>> > > *To:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Michael S. <mic...@ro...> - 2012-04-20 14:08:33
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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:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_mRNA/scf7180001235522/trackData.json status:404 dojo.js:14TypeError 2dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_CDS/scf7180001235522/trackData.json status:404 dojo.js:14TypeError 2dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_exon/scf7180001235522/trackData.json status:404 dojo.js:14TypeError 2dojo.js:14Error dojo.js:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Maker_gene/scf7180001235522/trackData.json status:404 dojo.js:14TypeError 2dojo.js:14Error dojo.js:14Error 2dojo.js:14Error ~/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:14Error jbrowse-min.js:1Error: Unable to load data/tracks/Augustus_match/scf7180001235522/trackData.json status:404 dojo.js:14TypeError 2dojo.js:14Error ________________________________ From: Robert Buels <rb...@gm...> To: Michael Stoker <mic...@ro...>; "gmo...@li..." <gmo...@li...> 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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *Cc:* "gmo...@li..." <gmo...@li...> > *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 <mic...@ro... > <mailto:mic...@ro...>> > > *To:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Robert B. <rb...@gm...> - 2012-04-20 14:02:11
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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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *Cc:* "gmo...@li..." <gmo...@li...> > *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 <mic...@ro... > <mailto:mic...@ro...>> > > *To:* "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Robert B. <rb...@gm...> - 2012-04-20 13:41:08
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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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...>; > "gmo...@li..." <gmo...@li...> > *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 <rb...@gm... <mailto:rb...@gm...>> > > *To:* Michael Stoker <mic...@ro... > <mailto:mic...@ro...>>; > > "gmo...@li... > <mailto:gmo...@li...>" > <gmo...@li... <mailto:gmo...@li...>> > > *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 <rb...@gm... <mailto:rb...@gm...> > <mailto:rb...@gm... <mailto:rb...@gm...>>> > > > *To:* Michael Stoker <mic...@ro... > <mailto:mic...@ro...> > > <mailto:mic...@ro... > <mailto:mic...@ro...>>> > > > *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 > > > > Gmo...@li... > <mailto:Gmo...@li...> > > <mailto:Gmo...@li... > <mailto:Gmo...@li...>> > > <mailto:Gmo...@li... > <mailto:Gmo...@li...> > > <mailto:Gmo...@li... > <mailto:Gmo...@li...>>> > > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > > > > > > > > > |
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From: Robert B. <rb...@gm...> - 2012-04-20 13:03:06
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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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...>; > "gmo...@li..." <gmo...@li...> > *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 <rb...@gm... <mailto:rb...@gm...>> > > *To:* Michael Stoker <mic...@ro... > <mailto:mic...@ro...>> > > *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 > > > Gmo...@li... > <mailto:Gmo...@li...> > <mailto:Gmo...@li... > <mailto:Gmo...@li...>> > > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > > > |
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From: Robert B. <rb...@gm...> - 2012-04-20 12:59:13
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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 <mic...@ro...> > *To:* "gmo...@li..." <gmo...@li...> > *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 > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Robert B. <rb...@gm...> - 2012-04-20 12:52:12
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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 <rb...@gm...> > *To:* Michael Stoker <mic...@ro...> > *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 > > Gmo...@li... <mailto:Gmo...@li...> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Michael S. <mic...@ro...> - 2012-04-20 09:49:08
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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? |
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From: Robert B. <rb...@gm...> - 2012-04-20 02:08:01
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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 > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Robert B. <rb...@gm...> - 2012-04-20 01:55:44
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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 > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Michael S. <mic...@ro...> - 2012-04-19 23:19:53
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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. |
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From: Michael S. <mic...@ro...> - 2012-04-19 23:01:48
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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? |
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From: Robert B. <rb...@gm...> - 2012-04-19 22:38:34
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Hi all, JBrowse 1.3.1 has been released, this is a minor release with fixes for some bugs found in 1.3.0. It can be downloaded from http://jbrowse.org/jbrowse-1-3-1-released/. Changes in this release: * Fixed memory-management bug that caused way too much RAM to be used by FeatureTrack loading (flatfile, bam, and biodb-to-json.pl) when loading with very large numbers of reference sequences. Big thanks to Tristan Lubinski for help in isolating this. * Fixed some bugs in BAM support section of setup.sh autosetup script, thanks to Tristan Lubinski for help in isolating this as well. * Added an example document with an iframe running JBrowse in embedded mode in docs/examples/embedded_mode.html * flatfile-to-json.pl now loads the ‘score’ attribute of features in the JSON. Rob -- Robert Buels Lead Developer JBrowse - http://jbrowse.org |
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From: Robert B. <rb...@gm...> - 2012-04-19 20:53:34
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Hi Tristan, (CCing to gmod-ajax for a public record) I've fixed the bam-to-json memory problem, thanks for your help today isolating it with me in person. It turned out to actually be a memory leak in the perl FeatureTrack formatting code that only manifests for large numbers of reference sequences. I'll be releasing 1.3.1 with the fix as soon as I can get it together, which is mostly a matter of how quickly I can write the release notes, blog post, Rob Robert Buels Lead Developer JBrowse - http://jbrowse.org On 04/19/2012 07:12 AM, Tristan Lubinski wrote: > Ahhh... Nevermind I figured it out... I was passing it a bam file that > was already sorted and indexed... apparently bam-to-json wants to do all > the work. Is there any way we can pass it a file that has already been > sorted and indexed or does that need to come from in order for jbrowse > to recognize it correctly? > > Tristan > > On Wed, Apr 18, 2012 at 11:16 PM, Tristan Lubinski <lub...@bu... > <mailto:lub...@bu...>> wrote: > > Hey Robert, > > i'm working on instaling jbrowse 1.3 and am having a problem getting > bam-to-json to work correctly... it keeps using up all 8 gigs of the > RAM I have available. The old version would run through the same > bam file on half the ram... What's going on? > > Thanks for any help you can offer, > Tristan > > |
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From: Robert B. <rb...@gm...> - 2012-04-19 13:04:08
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(CCing gmod-ajax support list for a public record) Wow, that's quite a dire subject line. :-) bam-to-json.pl actually already assumes that the input bam is sorted by start position. It does another sort by different criteria in order to put the features in nested-containment order so that it can generate nested-containment-list JSON for them. In the JBrowse 2.x release series, coming later this year, we're going to have a data backend that accesses BAM files directly instead of having this step of converting them to JSON (recorded in the JBrowse issue tracker as https://github.com/GMOD/jbrowse/issues/94) but we're not there yet. Robert Buels Lead Developer JBrowse - http://jbrowse.org On 04/19/2012 07:12 AM, Tristan Lubinski wrote: > Ahhh... Nevermind I figured it out... I was passing it a bam file that > was already sorted and indexed... apparently bam-to-json wants to do all > the work. Is there any way we can pass it a file that has already been > sorted and indexed or does that need to come from in order for jbrowse > to recognize it correctly? > > Tristan > > On Wed, Apr 18, 2012 at 11:16 PM, Tristan Lubinski <lub...@bu... > <mailto:lub...@bu...>> wrote: > > Hey Robert, > > i'm working on instaling jbrowse 1.3 and am having a problem getting > bam-to-json to work correctly... it keeps using up all 8 gigs of the > RAM I have available. The old version would run through the same > bam file on half the ram... What's going on? > > Thanks for any help you can offer, > Tristan > > |
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