WOMBAT – A program for Mixed Model Analyses by Restricted Maximum Likelihood

Examples under Windows

  • Q: I have downloaded the examples and am trying to run them under Windows, but WOMBAT fails straightaway, even for the simplest case. What is wrong ?
  • A: The examples have been produced under Linux. Windows/DOS and Linux differ in the `end-of-line' characters used. DOS uses a CR/LF (CR=Carriage return, LF=line feed) while Linux uses a LF only. Hence, a Linux file under DOS will be interpreted as a file with a single, long line – with obvious, disastrous consequences ! You need to `translate' the Linux files into Windows/DOS files before WOMBAT can run the examples. The tool for this is unix2dos. If this is not available on your machine, you can download a small program to do so from the web. Alternatively, there are web sites which allow you to do the conversion on-line, e.g. http://www.fileformat.info/convert/text/unix2dos.tr Under Ubuntu, look for todos
    N.B. You'll need to do this for all input files to WOMBAT, i.e. data, pedigree, parameter and any auxiliary files!
    The same holds for files generated under Windows to be used in a Linux run: the corresponding command is dos2unix or fromdos.

Linux runs using Excel data files

  • Q: I have installed WOMBAT under Linux and the examples all work just fine. Now I am trying to run my own analysis and nothing works. And, yes if it matters, my data file has been exported from Excel.
  • A: Yes, indeed that matters! Excel is a Windows program. Windows/DOS and Linux use different characters in a text file to denote the end of a line: CR/LF under DOS and LF under Linux, with CR standing for Carriage Return and LF for Line Feed. Hence, for any data, pedigree or parameter file created or edited under Windows and then ported to Linux, you need to remove the CR for WOMBAT to work properly. This is readily done using dos2unix which is a part of most Linux distributions (for newer versions of Ubuntu, try fromdos – you may have to install this first using something like sudo apt-get install tofrodos)

Windows run fails

  • Q: I am running WOMBAT under Windows, using the MinGW/MSYS version, by “double-clicking” on the file icon. That worked o.k. for the examples I tried, but now I am using my own data and .par file and all that happens is that it opens a window and immediately closes it gain without producing any output. What can I do?
  • A: You should really run WOMBAT from the command line in a DOS (or MinGW) window. Simply click on “Start” and then type “CMD” into the field under “Run” - this will open a DOS window for you. You can then run the program by typing wombat (if it resides somewhere where Windows looks for Program files) or Path_To_WOMBATDirectory\wombat if it is somewhere else (substitute the correct Path_To_WOMBATDirectory).
    If you have a problem, you should also specify the -v command line option. WOMBAT is quite fussy when checking your input and parameter files and stops with a 'programmed error stop' when it finds something that is not quite right. It also tries to write an explanatory message to the screen to tell you what to check. You miss out on all these messages (which have taken a great deal of effort to program) if you invoke the program by “double-clicking”. Good luck!
    Alternatively, if you really can't stand working with a command line interface, you could set up a simple .bat file (which you start by double-clicking) which opens a DOS window and runs WOMBAT, but does not close the window until you tell it to do so (see below for an example).
    rem Simple .bat file to run WOMBAT in a DOS window
    rem -> this assumes: 1) your parameter file is wombat.par
    rem                  2) any other run time options are given in the fist line of wombat.par
    rem                  3) wombat.exe resides in folder C:\Program_Files\WOMBAT
    @echo off
    color 70
    echo "Ready to run WOMBAT"
    pause
    C:\Program_Files\WOMBAT\wombat -v
    echo "WOMBAT has finished"
    pause
    exit

Larger examples under CYGWIN

  • Q: I am trying to run some of the larger examples under CYGWIN, but WOMBAT stops with a number of different messages, either telling me that it cannot allocate something, that there are too many equations or that I don't have enough RAM (which is nonsense, because I have 4GB). What can I do about this?
  • A: Change to Linux - this is your best option, especially if you have a modern 64-bit machine and want to be able to use all the RAM you have available for large analyses! Please read the caveats and compile notes for the Windows versions in the manual. In brief:
    • Both Windows versions of WOMBAT are 32-bit versions, i.e. even if there were no other restrictions, you would not be able to run any programs using more than 2GB of RAM.
    • Not all examples may run under Windows, as these versions of WOMBAT are restricted to a relatively small number of equations (150,000).
    • The `default' installation of CYGWIN limits the memory that can be allocated to any program to something which may be too small for the larger examples to run. You can change this; see the CYGWIN documentation for details, e.g. here (I have not tried this).
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