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

Question

I got a problem when run GSEA in command line:

the error is:

5290 [INFO ] Begun importing: Dataset from: fib2016_symbol.gct
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.rangeCheck(ArrayList.java:657)
        at java.util.ArrayList.remove(ArrayList.java:496)
        at edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:143)
        at edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:118)
        at edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:160)
        at edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:130)
        at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:747)
        at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:800)
        at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:788)
        at xtools.api.param.PobParam.getPob(PobParam.java:79)
        at xtools.api.param.DatasetReqdParam.getDataset(DatasetReqdParam.java:29)
        at xtools.gsea.Gsea.createHeader(Gsea.java:146)
        at xtools.gsea.Gsea.execute(Gsea.java:66)
        at xtools.api.AbstractTool.tool_main(AbstractTool.java:406)
        at xtools.gsea.Gsea.main(Gsea.java:140)

and my command line is:

java -Xmx5000m -cp /home/lucas_pkuhpc/lustre1/software/gsea-3.0.jar xtools.gsea.Gsea -res 190104GSEAinput/fib2016_symbol.gct -cls 190104GSEAinput/4GSEA.cls -gmx 190104GSEAinput/HALLMARK_DNA_REPAIR.gmx -collapse false -nperm 1000 -permute gene_set -rpt_label fib2016_symbol -metric log2_Ratio_of_Classes -s -plot_top_x 30 -gui false

I really do not know how to solve this problem, any suggestion and comment is welcome.

thanks

Answer 1

GCTParser line 140-143:

List colnames = ParseUtils.string2stringsList(currLine, "\t"); // colnames can have spaces

colnames.remove(0);                                 // first elem is always nonsense
colnames.remove(0);

If the coding is correct then there are not enough \\t (tab space) separators for colNames. There should be at least 1 for this error to not occur.