The first error message, du: cannot access `~skim': No such file or directory, made me curious. I think that if you reduce your program to a very simple command you'll find that it's not running from the right directory or that ~skim doesn't exist?

my $homedir = '~bogus';
$du=`du -ch $homedir`;
print "$du";
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produces a similar message for me:

./test
du: cannot access `~bogus': No such file or directory
0       total
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