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!
Hi Michael,
Would you be able to share a history back with these data and provided some notes about the dataset numbers linked to issues you observed for each/steps used to generate the issues? Then Jeremy our trackser designer can help me to find out what is going on. The number of scaffolds may be an issue - but I really cannot say without Jeremy's input.
You can send the link to just him and I. From the history menu (gear icon at top of right-most panel) ? pick Share or Publish, generate the link, and email it directly back off-list.
Sorry that you are having problems, but hopefully this can be worked out,
Jen Galaxy team
On 3/22/13 1:20 PM, Michael Axtell 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!
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 mja18@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:
To search Galaxy mailing lists use the unified search at:
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 james@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 mja18@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:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
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James Taylor -
Jennifer Jackson -
Michael Axtell