Fail to load sample data in my newly installed GSEA 3.0

[Zengli Guo]

Hi, 

I just installed the GSEA 3.0 in my MAC (Version 10.12.6) with Java 8 update 151. However I failed to load any expression dataset. I tried sample data of p53 set. I also changed the extension name as suggested in FAQ.  Any suggestions? Many thanks!

Please see the err information:

<Error Details>

---- Full Error Message ----

There were errors: ERROR(S) #:3

Parsing trouble

java.lang.IllegalArgumentExcepti ...

---- Stack Trace ----

# of exceptions: 3

------Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53.cls no known Parser for ext: ------

java.lang.IllegalArgumentException: Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53.cls no known Parser for ext: 

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:769)

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)

at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)

at javax.swing.SwingWorker$1.call(SwingWorker.java:295)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at javax.swing.SwingWorker.run(SwingWorker.java:334)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

------Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53_collapsed_symbols.gct no known Parser for ext: ------

java.lang.IllegalArgumentException: Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53_collapsed_symbols.gct no known Parser for ext: 

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:769)

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)

at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)

at javax.swing.SwingWorker$1.call(SwingWorker.java:295)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at javax.swing.SwingWorker.run(SwingWorker.java:334)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

------Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53_hgu95av2.gct no known Parser for ext: ------

java.lang.IllegalArgumentException: Unknown file format: /Users/zengliguo/Zengli @ Wan Lab/VprBP project/Young old VprBP RNA Seq analysis/Gene set analysis/p53 sample data/P53_hgu95av2.gct no known Parser for ext: 

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:769)

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)

at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)

at javax.swing.SwingWorker$1.call(SwingWorker.java:295)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at javax.swing.SwingWorker.run(SwingWorker.java:334)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)

[David Eby]

Hi,

Unfortunately, GSEA is unable to handle special characters in file names or paths, particularly spaces, and is most likely getting confused about the name of your file.  As it uses the file extension to determine the parser, it's unable to proceed.

I would suggest placing the input files into a folder with no spaces or special characters (like '@') in the name and work from there.  For GSEA, it's best to stick with alphanumeric characters plus the underscore in place of spaces.

It's a long-standing issue and we'd love to improve this, but with the age of the code base and our limited resources it's unlikely to be fixed in the near future.

Regards,

David

[Zengli Guo]

I see. The problem was solved when I moved the file to ./download folder. Thanks a lot

zengli

[ptangta...@gmail.com]

Hi,

I have solve the problem as your suggestion, but It still persistence like this

<Error Details>

---- Full Error Message ----

There were errors: ERROR(S) #:1

Parsing trouble

java.lang.IndexOutOfBoundsExcept ...

---- Stack Trace ----

# of exceptions: 1

------Index: 0, Size: 0------

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

at java.util.ArrayList.rangeCheck(Unknown Source)

at java.util.ArrayList.get(Unknown Source)

at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:101)

at edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:86)

at edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:748)

at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)

at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)

at javax.swing.SwingWorker$1.call(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at javax.swing.SwingWorker.run(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

at java.lang.Thread.run(Unknown Source)

please help to identify problem

Pat

[Anthony Castanza]

Hi Pat,

This is an extremely old thread, we generally ask that users create a new thread specific to their issue.

Are you still using GSEA 3.0? The current release of GSEA is 4.0.2 and we no longer offer direct support for GSEA 3.0. That said, it looks like something is malformatted with your .TXT input file. We have a specific format for .TXT files that GSEA can accept, please see our data format guidelines: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#TXT:_Text_file_format_for_expression_dataset_.28.2A.txt.29

-Anthony

Anthony S. Castanza, PhD

Curator Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[ptangta...@gmail.com]

Hi! Anthony

The problem all solved!   Thank you so much. I have two GSEA version in my computer, that probably cause the problem with my txt format too.  

-Pat