see printf and sprintf. You need to put %s in the print format for strings, %d for integers

while ( my $para = <$PROTFILE> ) { 
  # Remove fasta header line 
  if ( $para =~ s/^>(.*)//m ){ 
    $name = $1; 
  }; 
  # Remove comment line(s) 
  $para =~ s/^\s*#.*//mg; 
  # Trim trailing white space 
  $para =~ s/\s+$//; 
  # next FASTA_RECORD if $fasta_seen{ $para }++; 
  if ( $fasta_seen{ $para }++ ){ 
    printf "duplicate record %s %s \nwritten to %s\n",$name,$para,$out
+_filename; 
    print $OUTFILE '>'.$name.$para."\n\n";
  } 
}
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