failed data loading

[Ruifang Liu]

Hi, GSEA experts, 

I downloaded GSEA_MacApp_4.4.0-WithJava.app.zip, with Java for Apple Silicon Macs (M1 etc) for my macbook Pro, 14inch 2021. I had successfully loaded data and ran the software once. But I kept receiving error message when I tried it for the 2nd, 3rd, 4th times. 

I triple checked my java version, which is Java 8 Updata 451, which was last run on today (5/15/25).

Here is the error message, please help. 

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IllegalArgumentException: Unknown file format: /User ...

---- Stack Trace ----
# of exceptions: 1
------Unknown file format: /Users/ru40195/Library/CloudStorage/GoogleDrive-...@gmail.com/My Drive/T23-Pubs_Ideas-2025/2025-23c-GSEA/GSEA practice 3_051225/Input data/Phenotype labels.txt no known Parser for ext: liu------
java.lang.IllegalArgumentException: Unknown file format: /Users/ru40195/Library/CloudStorage/GoogleDrive-...@gmail.com/My Drive/T23-Pubs_Ideas-2025/2025-23c-GSEA/GSEA practice 3_051225/Input data/Phenotype labels.txt no known Parser for ext: liu
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:782)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:736)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

I also attached my files, please help do some internal check if possible. 

Best Regards,

Nancy

 

[Anthony Castanza]

Hi Nancy,

The issue here is that GSEA is failing to parse the mounted file path from the google drive folder, particularly, GSEA seems to be truncating at the @ symbol in the email address in the file path. I would recommend reading your files from a simple local path instead (e.g. your Documents or Downloads directory).

Additionally, as a note, I took a look at the files you sent, in the expression matrix file, you are using ensembl gene IDs for your identifiers, however these appear to be versioned ensembl IDs (e.g. ENSMUSG00000020218.11), if you are using our chip files to collapse your data to symbols for use with MSigDB gene sets (the recommended way to run this kind of data), you would need to trim the version suffix from the ID (ENSMUSG00000020218), if you don't trim those trailing version suffixes GSEA won't be able to match them to the identifiers in our mapping files. An easy way to do this is with a "text to columns" split in Excel if you aren't able to do this programmatically.

Let me know if you have any additional questions

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego