There were errors: ERROR(S) #:1 Parsing trouble java.lang.NumberFormatException: ...

[大川拓眞]

Hello!

I am having trouble loading my data on GSEA. To my knowledge, I have followed the formatting guidelines. I am not sure why I am receiving this message. I'm sure you can maintain confidentiality so I have attached the raw data file to the email. Please help me.

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.io.FileNotFoundException: / ...

---- Stack Trace ----
# of exceptions: 1
------/Users/okawatakuma/Desktop/Book3.txt (No such file or directory)------
java.io.FileNotFoundException: /Users/okawatakuma/Desktop/Book3.txt (No such file or directory)
    at java.base/java.io.FileInputStream.open0(Native Method)
    at java.base/java.io.FileInputStream.open(Unknown Source)
    at java.base/java.io.FileInputStream.<init>(Unknown Source)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:48)
    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)

Sincerely,

Takuma Okawa

[Anthony Castanza]

Hello,

In the first message the error is pointing to an invalid string in the header "GENE_SYMBOL".

The expected names for the first two columns are NAME and Description: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

instead of this you currently have FEATURE_ID and GENE_SYMBOL, which the parser isn't able to recognise.

This structure that you've used also expects that the filename will end with the extension ".gct", in the second error message you sent the parser is looking for, and failing to find, a file called "Book3.txt", I suggest clearing the load data window, then dragging and dropping the corrected file with the gct file extension in, and trying again.

Let me know if you still have issues after making these adjustments

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

Sincerely,

Takuma Okawa

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[Takuma Okawa]

Hello, 

Thank you for your reply.

>The expected names for the first two columns are NAME and Description: instead of this you currently have FEATURE_ID and GENE_SYMBOL, which the parser isn't able to recognise.

So, I changed the first columns like this(below↓). (And also I changed file name. It's not a big deal.) 

But the same errors occurred like this(↓) .

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble

java.lang.NumberFormatException: ...

---- Stack Trace ----
# of exceptions: 1

------For input string: "Description"------
java.lang.NumberFormatException: For input string: "Description"
    at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)
    at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source)
    at java.base/java.lang.Float.parseFloat(Unknown Source)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseStringToFloat(AbstractParser.java:250)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseFieldsIntoFloatArray(AbstractParser.java:361)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.AbstractParser.parseTextMatrixToDataset(AbstractParser.java:277)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:108)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:760)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:737)
    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)

> This structure that you've used also expects that the filename will end with the extension ".gct", in the second error message you sent the parser is looking for, and failing to find, a file called "Book3.txt", I suggest clearing the load data window, then dragging and dropping the corrected file with the gct file extension in, and trying again.

According to "Supported file formats", I thought that filename which end with the extension ".txt" is able to be used in this application.

Is this a misinterpretation?

And also, I'd like to know the way to convert ".txt" file to ".gct" file.

 

Sincerely,

Takuma Okawa

2022年7月19日火曜日 3:30:55 UTC+9 Anthony Castanza:

[Takuma Okawa]

Hello, 

I tried again with the filename which end with the extension ".gct.txt".

Then, I succeeded!!

Thank you again!!

Takuma Okawa

2022年7月20日水曜日 0:13:22 UTC+9 Takuma Okawa: