James, great! Glad you isolated the bug and will fix. It will come in handy for us (and maybe others).
Mike On Wed, Mar 27, 2013 at 2:07 PM, James Taylor <ja...@jamestaylor.org> wrote: > 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 >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- Michael J. Axtell, Ph.D. Associate Professor Dept. of Biology Penn State University http://axtell-lab-psu.weebly.com ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
