% cat output.txt
Chr	Coord	chip_id	subarray_id	gc	NA15510
1	475	5730	5730_1	0.6	0.266
1	505	5730	5730_1	0.63333333	0.422

...     ...     ...     ...             ...     ...

Chr	Coord	chip_id	subarray_id	gc	NA15510

...     ...     ...     ...             ...     ...

1	925	5730	5730_1	0.70666666	0.071
1	960	5730	5730_1	0.70333333	0.036

##</code><code>##

% cat t.pl
#!/usr/bin/perl -w
use strict;

my $filename = 'output.txt';
my %chr_arms = (
    1 => [ 1, 1000, 2000, 5000 ],
    2 => [ 1, 1000 ],
);

for my $chromosome ( sort { $a <=> $b } keys %chr_arms ) {
    if ( scalar @{ $chr_arms{$chromosome} } >= 2 ) {

        my $arm_start = shift @{ $chr_arms{$chromosome} };
        my $arm_end   = shift @{ $chr_arms{$chromosome} };

        print qq{Running Pipeline for $chromosome:$arm_start-$arm_end\n};

        # a long running process (written in C++)
        print qq{ask_bigdb [options] >> $filename\n}; ### OFFENDING LINE!!!

        redo;    # do the next arm of chromosome ...

    }

    # check output file is not empty
    if ( is_too_short($filename) ) {
        print qq{$filename is empty\n};
        next;
    }

    # a few more loooooooong running processes (written in C++ and Java)
    print qq{GC Normalize ...\n};
    print qq{Table merge ...\n};
    print qq{Median Normalize ...\n};
    print qq{Table merge ...\n};
    print qq{Wave Normalize ...\n};
    print qq{Table merge ...\n\n};

}

exit 0;

# Name      : is_too_short
# Purpose   : check if the file has more that one line in it
sub is_too_short {
    my $file = shift;

    # ensure the file exists
    if ( !-e $file ) {
        die qq{$file does not exist};
    }

    # now check its head-line-count
    if ( my $head = qx{head $file | wc -l} <= 1 ) {
        return 1;
    }
}