Running batch file error

I have already tried to find some solution on Java Essential forum, not much success there. I hope someone might suggest something here.
Design: one big file, split into chunks, recombined according to some order, feeded to some exe file, and finally compilation of results.
Problem: I can run that smoothly with jdk, however, when I use Java beans I am running into troubles. I can split the file, create an order, recombine the files, but when I try to feed it to an exe file(through a batch file) i get this error:
endfile record was detected in a READ statement (UNIT = 3). Error occurs at _MAIN__. A dubplicate file name exists or the file cannot be foundThe main method is something like this:
        s.split_ftn07() ;
        s.Define_Order() ;
        for (int i = 1 ; i < 11 ; i ++)
            s.re_combine(i) ;
            s.run_Fastran(i) ;
        s.ass_Result() ;my batch file:
@echo off
cd
"C:\JBoss\jboss-4.0.5.GA\bin\Fastran\FASTRAN.EXE"
ren FTN04 FTN04i
:finishand my method that runs the batch file: (as soon as it pass the exec(), it opens the cmd.exe windows and displays the error message).
public void run_Fastran(int x)
       try
           File ftn07_i = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\ftn07_" + x) ;
           File ftn07 = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\ftn07") ;
           ftn07_i.renameTo(ftn07) ;
           String path = "";
           path = "cmd /c start C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\FCall.bat";
           Runtime rt = Runtime.getRuntime();
           Process proc = rt.exec(path);
           String nameNew = "C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\FTN04-" + x + "-p12";//change p12 with the crack path input by user.
           File file = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\FTN04i");
           while (file.exists()==false)//until FTNO4i come into existence
            // File with new name
           File file2 = new File(nameNew);
            // Rename file
           file.renameTo(file2);
           File ftn07Back = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\ftn07") ;
           File ftn07_iBack = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\ftn07_" + x) ;
           ftn07Back.renameTo(ftn07_iBack) ;
           File ftn07_i_del = new File("C:\\JBoss\\jboss-4.0.5.GA\\bin\\Fastran\\ftn07_" + x) ;
           ftn07_i_del.delete() ;
       catch(Exception e)
           e.printStackTrace();
    }I am tired to figure out whats going on? Need some help here, will be greatly appreciated. Thanks

Thanks to all, I really appreciate all the pains which all of you have taken in resolving my problem.
It wasn't Java problem, rather batch file problem. I was only changing the directory, and was not providing for the exe file to run.
@echo off
cd  "C:\JBoss\jboss-4.0.5.GA\bin\Fastran"
"C:\JBoss\jboss-4.0.5.GA\bin\Fastran\FASTRAN.EXE"
ren FTN04 FTN04i
EXIT
:finishNow it is working fine.
I did check the access permissions, no problem with that I guess. The problem was with the path. The batch file couldnt go pass bin directory, and I noticed that only today ;(. At any rate, I changed that and now it is all smooth and dandy.
Once again, thanks a lot.

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