[Biojava-dev] Bug when reading FASTA file with many DNA Sequences

[Scooter Willis]

Daniel

You have two options. The first is to run java -Xmx2048m (the rest of your
parameters) and the out of memory error will go away. I have a Helper
method that will read the fasta file and lazy load when you request a
sequence. If you call this method

FastaReaderHelper.readFastaDNASequnece(File f, boolean lazySequenceLoad)
you will be able to load the entire fasta file with minimal memory
requirements.

Even though your fasta file is X when we load it into memory each sequence
position gets represented by a Java object so the memory footprint will be
larger.

Let me know if you don't have that particular method in the jars you are
using. Not sure of the latest release on jars. If you look in the
biojava3-genome module you will find examples of working with the DNA
sequences to translate proteins etc assuming you have CDS features to map
onto your sequences.

Thanks

Scooter

On 2/9/11 7:13 AM, "Mapleson Daniel Dr (CMP)" <D.Mapleson at uea.ac.uk> wrote:

>Hello,
>
>I'm trying to read a FASTA file that contains just over 4000 DNA
>sequences and is around 270MB big.  Each sequence starts like this:
>">SequenceName" followed by a linefeed.  The actual DNA sequence data
>does contain a linefeed every 40 characters or so.
>
>I want to read in the data into a LinkedHashMap object, similar to the
>example you specify in your cookbook:
>
>FileInputStream inStream = new FileInputStream(genomeFile);
>FastaReader<DNASequence, NucleotideCompound> fastaReader = new
>FastaReader<DNASequence, NucleotideCompound>(
>              inStream,
>              new GenericFastaHeaderParser<DNASequence,
>NucleotideCompound>(),
>              new 
>DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
>
>        try {
>            genomeData = fastaReader.process();
>        } catch (Exception ex) { }
>
>This works on some files but not the one containing the 4000 sequences.
>I get an exception generated by the JVM:
>
>Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC
>overhead limit exceeded
>        at 
>java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:45)
>        at java.lang.StringBuilder.<init>(StringBuilder.java:80)
>        at 
>org.biojava3.core.sequence.io.FastaReader.process(FastaReader.java:111)
>        at 
>workbench.Process_Hits_Patman.openFastaFile(Process_Hits_Patman.java:414)
>        at 
>workbench.Process_Hits_Patman.readFiles(Process_Hits_Patman.java:451)
>        at workbench.MirCat.openFile(MirCat.java:283)
>        at 
>workbench.MainMDIWindow.openMenuItemActionPerformed(MainMDIWindow.java:252
>)
>        at workbench.MainMDIWindow.access$000(MainMDIWindow.java:25)
>        at 
>workbench.MainMDIWindow$1.actionPerformed(MainMDIWindow.java:140)
>        at 
>javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
>        at 
>javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:231
>8)
>        at 
>javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java
>:387)
>        at 
>javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>        at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
>        at 
>javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1225)
>        at 
>javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItem
>UI.java:1266)
>        at java.awt.Component.processMouseEvent(Component.java:6263)
>        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
>        at java.awt.Component.processEvent(Component.java:6028)
>        at java.awt.Container.processEvent(Container.java:2041)
>        at java.awt.Component.dispatchEventImpl(Component.java:4630)
>        at java.awt.Container.dispatchEventImpl(Container.java:2099)
>        at java.awt.Component.dispatchEvent(Component.java:4460)
>        at 
>java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
>        at 
>java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
>        at 
>java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
>        at java.awt.Container.dispatchEventImpl(Container.java:2085)
>        at java.awt.Window.dispatchEventImpl(Window.java:2475)
>        at java.awt.Component.dispatchEvent(Component.java:4460)
>        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
>        at 
>java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.ja
>va:269)
>        at 
>java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:
>184)
>
>The amount of memory on the system isn't an issue.  I tried this on a
>machine with 12GB of RAM.  It seems to be an issue with the garbage
>collector getting tired of deleting temporary objects!  Also I noticed
>that although the file is less than 300MB large, the actual amount of
>heap space used increases from 100MB to over 900MB when in
>FastaReader.Process before the exception occurs.
>
>Unfortunately I can't share the FASTA file that is causing the problem.
>
>Would it be possible for you guys to look into this and either produce a
>fix or suggest a workaround?  Also do you think there is someway to
>optimise the performance and memory usage of this process?
>
>Finally, I have a question about selectively loading sequences from a
>FASTA file.  The idea being to reduce memory usage.  Is it possibility to
>do this using biojava?  i.e. given a DNA sequence name, only load that
>sequence into memory?  Or do we have to load the entire FASTA file into a
>LinkedHashMap each time?
>
>Thanks in advance for your help on this one,
>
>Best regards,
>Dr Daniel Mapleson (UEA)
>
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