Do your files have empty lines which don't match your regexps? Try returning empty list (()) in case the regexp didn't match (map will omit the element in this case): 
$ perl -w -MData::Dumper -E'%h = map {if(/(.+)\s+\|\s+(.+)/){$1=>$2}el
+se{()}} (<>); print Dumper \%h'
Q6GZX4 | PF04947.9
Q96355 | PF01486.12 PF00319.13
Q96356 | PF01486.12 PF00319.13
Q39371 | PF01486.12 PF00319.13

DSFSDF ASD SSSSSSSSSS
^D
$VAR1 = {
          'Q96355' => 'PF01486.12 PF00319.13',
          'Q96356' => 'PF01486.12 PF00319.13',
          'Q6GZX4' => 'PF04947.9',
          'Q39371' => 'PF01486.12 PF00319.13'
        };

[download]
Edit: return an empty list
Sorry if my advice was wrong.

In reply to Re^3: Debugging help! by aitap
in thread Debugging help! by invaderzard

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