System, as you said, returns 0 when execution is successful. Therefore the lines: 
if(!system("$program>$seq_file")) { 
      # not //;)   error
 }

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Aren't correct. Because When the return of system is false, as you check in the condition, there's no error. I think you should drop the !..

In reply to Re: SYSTEM call on windows misbehaves by Ido
in thread BSYSTEM/B call on windows misbehaves by Cheburashka

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