GSEA not working

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Matthew Cserhati

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Nov 20, 2018, 11:12:48 AM11/20/18
to GenePattern Help Forum
Hello GenePattern forum,

I am trying to run GSEA on te GenePattern website: https://genepattern.broadinstitute.org/gp/pages/index.jsf
My job id is 1750490. I keep getting the following error:


java.lang.IllegalArgumentException: <html>
<body>
<p>No template for name: 9HCCpats_RPKM_allSamples.cls#9lat_test2</p><p>The Available templates are:</p>
9HCCpats_RPKM_allSamples.cls<br>
9HCCpats_RPKM_allSamples.cls#NML_versus_TUM<br>
9HCCpats_RPKM_allSamples.cls#TUM_versus_NML<br>
9HCCpats_RPKM_allSamples.cls#NML<br>
9HCCpats_RPKM_allSamples.cls#TUM<br>
</body></html>
	at edu.mit.broad.genome.parsers.ParserFactory.findTemplate(ParserFactory.java:1033)
	at edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:298)
	at edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:273)
	at xtools.api.param.TemplateSingleChooserParam._getTemplates(TemplateSingleChooserParam.java:142)
	at xtools.api.param.TemplateSingleChooserParam.getTemplate(TemplateSingleChooserParam.java:52)
	at xtools.gsea.Gsea.execute(Gsea.java:69)
	at xtools.api.AbstractTool.tool_main(AbstractTool.java:406)
	at xtools.gsea.Gsea.main(Gsea.java:140)
	at org.genepattern.modules.gsea.GseaWrapper.main(GseaWrapper.java:362)

I tried creating the cls file with the ClsFileCreator module for my .gct file.
I even tried re-running GSEA with some files that I knew had worked previously, but those also failed (job # 1750489).

Is something wrong with the server? I think I've gotten the file format right, I just don't understand why I keep getting this error.

Thanks, Matthew

===================

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong):

Job ID if run on a publicly available server.

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?
   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right hand corner of the module input page or here: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
* GenePattern  Videos - http://software.broadinstitute.org/cancer/software/genepattern/video-tutorials
* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

Barbara Hill

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Nov 20, 2018, 7:55:40 PM11/20/18
to GenePattern Help Forum
Hello Matthew, 

Both of the jobs you cited seem to have been deleted.

Were you able to resolve your error?

Best
-Barbara
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