Your exec is probably failing in the same way, but something is keeping you from seeing the error. When you use multiple arguments like that, you are responsible for doing your own argument breakup. Whitespace is no longer significant. Perhaps you want: 
system $musclepath, "-in", $inpath, "-out", $outpath, "-stable";
if ($?) { ... something broke, deal with it ... }

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-- Randal L. Schwartz, Perl hacker
Be sure to read my standard disclaimer if this is a reply.

In reply to Re: system does not work but exec. why? by merlyn
in thread system does not work but exec. why? by Anonymous Monk

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