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I am unable to reproduce the stated problem. Furthermore, after removing the debug print statements (e.g. say qq(DEBUG: Line = "$line");), the output I get is:
Coordinate No of Strains AA Change
703 1 AA Ala->Thr
937 1 AA Val->Leu
1804 3 AA Ser->Thr
This appears to be exactly what you were hoping for!
Please check that the code and data you've posted is the same as that which generates the warnings you described.
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