You cannot determine whether an error occurred or not based on whether $! is not because $! is meaningless if no error occurred.

eval won't help as it catches exceptions and backticks do not throw exceptions.

Backticks are documented to return undef on error, so what you need is 

my $result = `blastall -i foo -o bar -p blastx -d baz`;

die("Could not execute blastall: $!\n")
   if !defined($result);

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In reply to Re: Capture external program return value by ikegami
in thread Capture external program return value by llancet

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