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  • CAP3 cygwin doesn't work.

    I'm trying to assemble FASTA sequences with CAP3 on Windows using Cygwin.
    I have cap3.cygwin.tar from http://seq.cs.iastate.edu/cap3.html. Cygwin works fine as far as I can tell.

    cap3.exe appears to do nothing. No errors, no output. This is what happens when I run the example:

    Code:
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $ ls
    README  xyz  xyz.con  xyz.qual
    
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $ cat README
    The command for running cap3 on data set xyz
    
       ../cap3   xyz  >  xyz.out &
    
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $ ../cap3 xyz > xyz.out &
    [1] 5048
    
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $
    [1]+  Exit 127                ../cap3 xyz > xyz.out
    
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $ cat xyz.out
    
    edward.siefker@PD7RIZZOLAB3 ~/edward.siefker/Documents/CAP3/example
    $
    Bash returns exit code 127. Google tells me this means something is "not found". But I have no leads as to what that might be. Any ideas?

  • #2
    "something" being "command". That is, "command not found". Could we see the result of:

    ls ../cap3

    If that exists, then try:

    chmod +x ../cap3

    prior to rerunning your command.
    --
    Phillip

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