$site_length_catch{$key1}[$key4]

Did you mean for that to be an array ref instead of a hash ref for $key4? Also, what values does $key4 take?

If $key4 happens to be a large number, then you'll blow away all your memory in one step as the array attempts to grow to ludicrous size.

In reply to Re: Memory issue with large cancer gene data structure by Anonymous Monk
in thread Memory issue with large cancer gene data structure by ZWcarp

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