Hi, Have you tried increasing the size of the heap? You can use the -Xmx option to java, e.g. -Xmx2048m or higher.
The GC overhead error is usually thrown when the constraints of the heap size force the JVM to spend too much time collecting garbage. -da On Wed, Jun 27, 2012 at 12:01 AM, Haluk Dogan <[email protected]> wrote: > Hi, > > I have an 1.8 GB fasta file and I was trying to read it with the following > code as in suggested examples page. > > LinkedHashMap<String, DNASequence> seqs = > FastaReaderHelper.readFastaDNASequence(new File(args[0])); > > I don't get any error for small size files but it gives the following error > for big files. > > Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit > exceeded > at java.util.Arrays.copyOf(Arrays.java:2746) > at java.util.ArrayList.ensureCapacity(ArrayList.java:187) > at > > org.biojava3.core.sequence.storage.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:187) > at > > org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88) > at org.biojava3.core.sequence.DNASequence.<init>(DNASequence.java:81) > at > > org.biojava3.core.sequence.io.DNASequenceCreator.getSequence(DNASequenceCreator.java:62) > at > org.biojava3.core.sequence.io.FastaReader.process(FastaReader.java:113) > at > > org.biojava3.core.sequence.io.FastaReaderHelper.readFastaDNASequence(FastaReaderHelper.java:106) > at > > org.biojava3.core.sequence.io.FastaReaderHelper.readFastaDNASequence(FastaReaderHelper.java:118) > > > Is there any efficient way? > > Thanks in advance. > > -- > HD > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
