math - different results of 2 sample kolmogorov-smirnov gof matlab -

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I have done a GOF test in matlab, but two samples of Kolloggorov Smirnov test gave me the opposite result in Matlab I use this code. Done 
  file = importdata ('all_subj_1file.xls', '\ t'); [Ill1] = xlsread ('all_subj_1file.xls', 'ill1', 'b2: e1608'); Ill1_frac = ill1 (:, 2); [A, b] = gamfit (ill1_frac); Y = gamrnd (a (1), a (2), 1607,1);   
 But from time to time I get different  p  and  ks2stat  also (probably because whenever I run the code I also create new flaws).  The question is  How do I choose the result of Kolmogorov-Smernov? Should I run the code multiple times and should I like the most? But they are opposite (like deviations or H1 levels).   
 
 
 A sample Kolmogorov Smirnov should be tested to get GOF of theoretical distribution instead of using two sample KS tests Can be done

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