Failed to use system () and win 10 bash.exe in Matlab

I am trying to use new bash functionally from windows 10 to run a linux program through matlab.

In this particular case, it is a program called snaphu that processes the input file and generates the output file. On linux (or the new bash shell in win10), you start it like:

snaphu -f configfile inputfile

      

        
        
        
      

    

You can run this command directly in cmd with:

bash -c "snaphu -f configfile inputfile"

      

        
        
        
      

    

This process processes the file and generates an output file. I am using matlab to create an input file and I would like to run snaphu after creating this file with

system('bash -c "snaphu -f configfile inputfile"')

      

        
        
        
      

    

use matlab to process the output file it generates in a single worker thread. However, using this command, I am not getting my output file. However adding and working.

system('bash -c "snaphu -f configfile inputfile" &')

      

        
        
        
      

    

The problem with this approach is that I am using a for loop to process about 1000 of these input files, each different from the last iteration. If I use "&" every time a new window opens.

I don't understand why it generates an output file in the latter case, but not the first. Can anyone help me?