[Biojava-l] Sequence object size: the sequel...

[Schreiber, Mark]

Hi -
 
This is almost certainy because the memory allocated to the JVM at start up has been exceeded by importing such a large sequence.
 
A simple solution is to allocate more memory to your JVM using the -Xms option:
 
       java -Xms1024M WECBFinder
 
this will start your program with 1024M (1G) allocated to the JVM stack. Consult you JVM extended features help for the exact syntaxt for your JVM.
 
- Mark
 

	-----Original Message----- 
	From: Sylvain Foisy [mailto:sylvain.foisy@bioneq.qc.ca] 
	Sent: Sat 19/10/2002 3:52 a.m. 
	To: biojava-l@biojava.org 
	Cc: 
	Subject: [Biojava-l] Sequence object size: the sequel...
	
	

	Hi,
	
	I found why my program would crash with IndexOutOfBound error. I now
	have a different problem. Here is my little program for parsing genomic
	contigs as found at ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens. I am
	using the .fa file for each chromosome.
	
	import java.io.*;
	import org.biojava.bio.symbol.*;
	import org.biojava.bio.seq.*;
	import org.biojava.bio.seq.io.*;
	
	public class WECBFinder
	{
	  public static void main(String[] args)throws IOException
	  {
	    BufferedReader inFile;
	    PrintWriter outFile;
	    Sequence seq;
	    String sequence=" ";
	    String lePath=" ";
	    int chr;
	    int nbSequences=0;
	
	    try
	    {
	      System.out.println("Programme de recuperation de sequences
	provenant du genome humain");
	      System.out.print("Entrer le chromosome desire: ");
	
	      BufferedReader stdin=new BufferedReader(new
	InputStreamReader(System.in));
	      chr=Integer.parseInt(stdin.readLine());
	      System.out.println("Recuperation de la sequence du chromosome "+
	chr);
	
	      lePath="/databanks/h_sapiens_chr/hs_chr"+chr+".fa";
	
	      inFile=new BufferedReader(new FileReader(lePath));
	
	      SequenceIterator stream=SeqIOTools.readFastaDNA(inFile);
	
	      while(stream.hasNext())
	      {
	        seq=stream.nextSequence();
	        System.out.println(seq.getName());
	        System.out.println(seq.subStr(1,10));
	        System.out.println(seq.subStr(seq.length()-9,seq.length()));
	        nbSequences++;
	      }
	
	      System.out.println("Fin de la lecture du fichier contenant le
	chromosome "+chr);
	      System.out.println("Nbre de sequences individuelles dans le
	fichier: "+nbSequences);
	    }
	
	    catch (Exception e)
	    {
	      System.err.println(e);
	      e.printStackTrace();
	    }
	  }
	}
	
	If I try with chromosome 18, it works very well. When I am using
	chromosome 22, I get a java.lang.OutOfMemoryError message. My machine
	has 1GB of RAM; I tried it on a 2 GB machine and it works.
	
	Anybody knows a way to make Sequence objects smaller of to circumvent
	this problem? I am writing each Sequence object to its own file and then
	flushing it to make space for the next one...
	
	I plead guilty: I am considering myself pretty new using BioJava.
	
	Cordially
	
	Sylvain
	
	 
	
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