Ignoring the fact that the line inside the while loop is not valid perl, if it were in a shell script, I submit that it would be a contender for the Useless cat award since

cat /mnt/scripts/lagtime/tmp/input.txt |awk '{printf "%1.50s\t%0.60s\t
+%0.45s\t %0.45s\n", $1, $2, $3, $4}' | sh /mnt/scripts/lagtime/calcul
+ate_lag.sh > /tmp/snapvault_status.out.out;
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is identical to

awk '{printf "%1.50s\t%0.60s\t%0.45s\t %0.45s\n", $1, $2, $3, $4}' /mn
+t/scripts/lagtime/tmp/input.txt | sh /mnt/scripts/lagtime/calculate_l
+ag.sh > /tmp/snapvault_status.out.out;
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Moreover, elsewhere, you claim that Awk is needed to put the columns in the right place... - a palpably untrue claim since you're simply using awk to strip out and re-format the first 4 columns, leaving the ordering untouched.

The problem is that the last output file is empty - this shouldn't come as a huge surprise if the last of the input lines causes an empty line to be written to the output - via the /mnt/scripts/lagtime/calculate_lag.sh script - since, within the loop, the output file is rewritten, c/w being appended to, each time.

In the light of this, I think I'd be tempted to

1. Modify /mnt/scripts/lagtime/calculate_lag.sh to take a single line as an argument
2. Coalesce the ssh invocations with the awk command
3. Finally, to re-write it [the snippet] something along the following lines i.e. untested:

use warnings;
use strict;

use autodie;

my @HOSTS = qw/datab01 datab02 datab03/;
my $IN_FILE = q(/mnt/scripts/lagtime/tmp/input.txt);
my $OUT_FILE = q(/tmp/snapvault_status.out.out);

open IN_FILE, qq/>$IN_FILE/;

foreach my $host (@HOSTS) {
    foreach (`ssh $host snapvault status | tail -n +3`) {
        local @_ = split; # Avoid warnings
        printf IN_FILE "%1.50s\t%0.60s\t%0.45s\t %0.45s\n", $_[0], $_[
+1], $_[2], $_[3];
    }
}

close IN_FILE;

open IN_FILE, qq/<$IN_FILE/;
open OUT_FILE, qq/>$OUT_FILE/;

while (<IN_FILE>) { print OUT_FILE `sh /mnt/scripts/lagtime/calculate_
+lag.sh $_` }

close IN_FILE;
close OUT_FILE;
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