$file won't interpolate inside q{}. A handful of alternatives:

• $command = "pax -r -f $file -s'!DirPart1.DirPart2.DirPart3/SubDir/!/data/kev/atlanta/emtex/invoices/!p'"
• $command = qq{pax -r -f $file } . q{-s'/DirPart1.DirPart2.DirPart3\/SubDir\//\/data\/kev\/atlanta\/emtex\/invoices\//p'};
• $command = sprintf q{pax -r -f %s -s'/DirPart1.DirPart2.DirPart3/SubDir\//\/data\/kev\/atlanta\/emtex\/invoices\//p'}, $file;
• $command= q{pax -r -f $file -s'/DirPart1.DirPart2.DirPart3/SubDir\//\/data\/kev\/atlanta\/emtex\/invoices\//p'}; $command =~ s/\$file/$file/;

Or something else.

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