Question: Galaxy Phyloviz Error Visualizing Nexus File
gravatar for danielfortin86
3.4 years ago by
United States
danielfortin86100 wrote:

I'm having a problem displaying NEXUS files in Galaxy's Phyloviz viewer.  Any help would be greatly appreciated. When I try and view the simple nexus file I get the error below:

Error Traceback:

View as:   Interactive  |  Text  |  XML (full)

IndexError: list index out of range


Module weberror.evalexception.middleware:364 in respond         view
>>  app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__         view
>>  return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__         view
>>  return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__         view
>>  return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request         view
>>  body = method( trans, **kwargs )

Module galaxy.webapps.galaxy.controllers.visualization:1010 in phyloviz         view
>>  data = pd.get_data( tree_index=tree_index )

Module galaxy.visualization.data_providers.phyloviz:36 in get_data         view
>>  jsonDicts, parseMsg = nexusParser.parseFile( file_name )

Module galaxy.visualization.data_providers.phyloviz.nexusparser:15 in parseFile         view
>>  return self.parseNexus(filePath)

Module galaxy.visualization.data_providers.phyloviz.nexusparser:65 in parseNexus         view
>>  key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'","") #replacing illegal json characters

IndexError: list index out of range

Nexus File:

[R-package APE, Mon Oct 27 17:31:54 2014]

      1  GCA_000003215,
      2  GCA_000027105,
      3  GCA_000450925,
      4  GCA_000449745
   TREE * UNTITLED = [&U] (4:0.0001390332429,3:9.926730628e-05,(1:1.873724177e-05,2:3.650049072e-06):0.008631185479);


software error galaxy • 872 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson24k • written 3.4 years ago by danielfortin86100
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:


This error indicates that an expected line of the input was not found during the tool execution. Input format is generally the first place to look for the root cause. If you modify the format of the input to be exactly within specification (and assign the datatype, if you have not done this already) does it help?

For example, change the header from: 

[R-package APE, Mon Oct 27 17:31:54 2014]


To be:


You can do this before upload, or by using a combination of dataset line selection tools in the tool group "Text Manipulation".

This is a bit of a laundry list of ways to correct inputs/errors, but it may be helpful.

It is how I begin troubleshooting. Please note that all datatypes are not in the wiki 'Datatypes' link, just the most commonly used. But this is a wiki, please feel free to edit and add it in! To see all defined datatypes within Galaxy: click on the pencil icon for a dataset, then in the center panel go into the tab "Datatype" to search. If a datatype is listed here, it available on the instance you are working on. Nexus is defined on the public Main Galaxy instance at

Please let us know if this resolves the issue or not, Jen, Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson24k

I tried deleting the extra line as you suggested, but I still get the same error. I'm kind of at a loss to figuring out why it doesn't work. I've tried opening this in other viewers and it accepts them. Any additional help would be greatly appreciated

ADD REPLYlink written 3.3 years ago by danielfortin86100
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