This 

 tempProteinFamFileCreator();
...
sub tempProteinFamFileCreator 
{
my $infile = $ARGV[0]."_ProFam";

[download]

is more generically written as 

...
tempProteinFamFileCreator( @ARGV );
...
sub tempProteinFamFileCreator {
    my  $infile   = $_[0] .'_ProFam';
# or
#   my  $infile   = shift .'_ProFam';


...

[download]

Now sub tempProteinFamFileCreator doesn't depend on @ARGV :) after all, you wouldn't write 

 @ARGV = ( 1 , 2 , 3 );
print @ARGV;

[download]
instead of 
print 1,2,3;

[download]

In reply to Re: -s testing for empty file; works on local, but not on remote by Anonymous Monk
in thread -s testing for empty file; works on local, but not on remote by Jeri

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