If my Google searches results are correct, the "SAM header is present" line comes out on STDOUT. The backticks will capture STDOUT by default but with some redirection, we can make it only capture STDERR where real errors should show up. See http://perldoc.perl.org/perlop.html#`STRING` for more details.

# discard STDOUT but capture STDERR in @out
my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1 1>/dev/null`; 
print OUT @out;
[download]

If you really do want the "SAM header is present" line to come out on STDOUT then you could do something like this.

# redirect STDOUT to stdout.log and capture STDERR in @out
my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1 1>stdout.log`;
print OUT @out;
my $stdout = do { local( @ARGV, $/ ) = 'stdout.log'; <> }; # slurp the
+ contents of stdout.log into $stdout
print $stdout;
[download]

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