title: Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
body: <p>I can't run my process. It gives the following exception: "Exception in thread "main" java.lang.OutOfMemoryError: Java heap space"</p>
  
  <blockquote>
    <p>java -Xms32m -Xmx516m FilteringSNP_genus
    Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
            at java.util.Arrays.copyOf(Arrays.java:2882)
            at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100)
            at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:515)
            at java.lang.StringBuffer.append(StringBuffer.java:306)
            at java.io.BufferedReader.readLine(BufferedReader.java:345)
            at java.io.BufferedReader.readLine(BufferedReader.java:362)
            at FilteringSNP_genus.main(FilteringSNP_genus.java:65)</p>
  </blockquote>
  
  <p>I have tried different memory usage configurations like:</p>
  
  <blockquote>
    <p>java -Xms32m -Xmx1024m FilteringSNP_genus</p>
  </blockquote>
  
  <p>but it has not worked, and increasing the -XmxVALUE has given a GC overheadlimit exceeded exception:</p>
  
  <blockquote>
    <p>Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
            at java.lang.String.substring(String.java:1940)
            at java.util.StringTokenizer.nextToken(StringTokenizer.java:335)
            at FilteringSNP_genus.main(FilteringSNP_genus.java:77)</p>
  </blockquote>
  
  <p>Could anyone provide some clue to fix this?</p>
  
  <p>Thanks</p>