Re: reading fasta file out of memory error

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
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