First, I think you might have an error in the code you submitted. I assume that

$names{$refnum} = $str;
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should be

$names{$ref} = $str;
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Second, the reason the code is dying is because on the last line,  $names{$number} does not exist.

It might be a good idea to take a look at what $names is actually holding after the loop. A good way to see that is to use Data::Dumper

#!/usr/bin/perl

use Data::Dumper;

%names;
{
   open(name, "<data/gly.txt");
   while(<name>) {
      ($ref, $str) = split /\|/;
      $names{$ref} = $str;
   }
}
 
print Dumper(%names);
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This will help you track down the problem.

davidj