[Gmod-ajax] BigWig Wiggle XY - not working for large bw files

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] BigWig Wiggle XY - not working for large bw files

Keiran Raine
Hi,

I've got BW files for pulldown and genomic data and I'm finding that the pulldown (exome sequencing) files are rendering fine, ~400 MB, but fails when wholegenome scale files are used with the following error:

416 (Requested Range Not Satisfiable) when attempting to fetch…

A more detailed analysis seems to indicate the tipping point is for files between 2.1GB and 5.1GB.  Different zoom levels don't appear to make a difference, although the following error occurs below 10kb for a 5.1 GB file, but the initial error is maintained on a 18GB file down to bp resolution:

TypeError: Cannot read property 'value' of undefined

Feel free to ask for further details or send me patches to test (I may be able to make the bw files available via ftp if needed).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: BigWig Wiggle XY - not working for large bw files

Keiran Raine
Added this to the big tracker on GitHub

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 28 Aug 2013, at 00:11, Keiran Raine <[hidden email]> wrote:

Hi,

I've got BW files for pulldown and genomic data and I'm finding that the pulldown (exome sequencing) files are rendering fine, ~400 MB, but fails when wholegenome scale files are used with the following error:

416 (Requested Range Not Satisfiable) when attempting to fetch…

A more detailed analysis seems to indicate the tipping point is for files between 2.1GB and 5.1GB.  Different zoom levels don't appear to make a difference, although the following error occurs below 10kb for a 5.1 GB file, but the initial error is maintained on a 18GB file down to bp resolution:

TypeError: Cannot read property 'value' of undefined

Feel free to ask for further details or send me patches to test (I may be able to make the bw files available via ftp if needed).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
------------------------------------------------------------------------------
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax