Error when running GSEAPreranked

[dlahr.fo...@gmail.com]

Hello

I'm trying to run GSEAPreranked on cloud.genepattern.org and I get the follow error:

java.lang.ClassCastException: edu.mit.broad.genome.objects.DefaultDataset cannot be cast to edu.mit.broad.genome.objects.RankedList

	at xtools.api.param.RankedListReqdParam.getRankedList(RankedListReqdParam.java:28)
	at xtools.gsea.GseaPreranked.createHeader(GseaPreranked.java:182)
	at xtools.gsea.GseaPreranked.execute(GseaPreranked.java:74)
	at xtools.api.AbstractTool.tool_main(AbstractTool.java:406)
	at xtools.gsea.GseaPreranked.main(GseaPreranked.java:176)
	at org.genepattern.modules.gseapreranked.GseaPrerankedWrapper.main(GseaPrerankedWrapper.java:298)
java.lang.ClassCastException: edu.mit.broad.genome.objects.DefaultDataset cannot be cast to edu.mit.broad.genome.objects.RankedList
	at xtools.api.param.RankedListReqdParam.getRankedList(RankedListReqdParam.java:28)
	at xtools.gsea.GseaPreranked.execute(GseaPreranked.java:77)
	at xtools.api.AbstractTool.tool_main(AbstractTool.java:406)
	at xtools.gsea.GseaPreranked.main(GseaPreranked.java:176)
	at org.genepattern.modules.gseapreranked.GseaPrerankedWrapper.main(GseaPrerankedWrapper.java:298)

(link to above:  https://cloud.genepattern.org/gp/jobResults/104307/stderr.txt)

Job ID:  104299

Any help / advice you can give would be greatly appreciated.

Thank you,

Dave

[Barbara Hill]

Hi Dave,

Nice to see you here! Though, I'm sorry you are having trouble.

Looks like you need to change your txt extensions to rnk.

From one of the developers, in a previous private thread:

"What's happening is that GSEAPreranked is getting confused by the TXT extension

on your input file. Internally, the GSEA code decides which dataset file parser
to use based on the extension and so it's using our TXT parser. The TXT parser
requires a quite specific format and assumes a multi-sample format which is not
valid for GSEAPreranked in any case.

Try renaming your input file to have the RNK extension and give it another try."

Let us know if that works!

All the best

-Barbara

[dlahr.fo...@gmail.com]

Hi Barbara

Good to see you too, thank you for the quick response - that fixed it for me.  I have notes written up but for got to explicitly mention the .rnk extension; I've added it now in bold :).  Also FYI / this may be known, I ran out of heap space with the default (2 GB) setting, upping to 4 GB worked.

Cheers,

Dave

[Barbara Hill]

Glad that worked!

We'll keep an eye on resources usage and see if that should generally be set higher.

Thanks!

-Barbara