try {
			// Open or create the output file
	        FileOutputStream os = new FileOutputStream(this.clustalOutputFile);
	        FileDescriptor fd = os.getFD();
	        
	        if (this.process != null) {
	        	this.process.getInputStream().close();
	        	this.process.getOutputStream().close();
	        	this.process.destroy();
	        }
			this.process = Runtime.getRuntime().exec(cmdarray);
			
			 // Flush the data from the streams and writers into system buffers.
	        // The data may or may not be written to disk.
	        os.flush();
	        this.process.getOutputStream().close();
	        // Block until the system buffers have been written to disk.
	        // After this method returns, the data is guaranteed to have
	        // been written to disk.
	        fd.sync();
		} catch (Exception e) {
			e.printStackTrace();
		}