Hi Michael, sorry it took a while but we've figured out the root cause
of this issue and will be deploying a fix shortly. Thanks!

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Fri, Mar 22, 2013 at 4:20 PM, Michael Axtell <mj...@psu.edu> wrote:
> Hi everyone.
>
> I'm having an issue with a wiggle file.  I'm using Trackster on the
> public-main instance of Galaxy, with a custom genome build. My wiggle
> file fails to be shown. When added to the visualization using the 'add
> tracks' dialog, I see the usual hatched gray lines with the message
> "processing data, this may take some time".  But then after a few
> minutes the track just goes to hatched gray lines with no messages,
> and the intensities are never displayed, nor is any error message (or
> any message at all, just stuck with the hatched gray lines).
>
> The .wig file has been extensively validated to conform to UCSC spec.
> In addition, the same file displays data just fine when loaded into
> Broad's IGV. So I'm confident it is formatted correctly.
>
> The custom genome is not a great one .. scaffolds not pseudomolecules,
> and there are many thousands of scaffolds in the assembly (scaffold
> N50 is 1.3M at scaffold 111 out of ~2,100 scaffolds; total length
> ~480M). If I slice my problematic wiggle file to only keep
> sub-sections of the data, sometimes it works.  I tested a number of
> such sub-slices, and some worked and some didn't, as below (the
> numbers refer to scaffold numbers in my custom genome):
>
> 1-50 : worked
> 1-100 : worked
> 1-200 : worked
> 1-300 : failed
> 1-400 : failed
> 1-500 : failed
>
> 100-250 : worked
> 200-300 : worked
> 300-400 : worked
> 500-600 : worked
>
> >From the above, it seems possible the error is that Trackster just
> doesn't like wig files that exceed a certain number of
> chromosomes/scaffolds? Or some sort of data overload issue?
>
> Some other information: This custom genome build works fine on
> trackster to visualize several other datasets in gff, gff3, and bed
> format. In addition, the problem wiggle file is not so large .. the
> full file is only ~48M. It is a fixedStep file with span and step both
> equal to 100, and the data are relatively sparse.
>
> If anyone has a clue, let me know .. thanks!
>
> --
> Michael J. Axtell, Ph.D.
> Associate Professor
> Dept. of Biology
> Penn State University
> http://axtell-lab-psu.weebly.com
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___________________________________________________________
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