It is probable that one of the values of $giName, $gssName, $definition or $sequence are not defined (NULL) in the line

print FILE ">$giName $gssName $definition\n$sequence";
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I guess that the data contains some NULL columns. Also you might be better off writing the:

( my $giName, my $gssName, my $definition, my $sequence )
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as

my ($giName,$gssName,$definition, $sequence )
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/J\