# Put fields in Array[counter]
    $Arrays[$counter] = split /\t/, $line;
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I think you meant:

    $Arrays[$counter] = [ split /\t/, $line ];
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or even (with autovivification) — though I consider that less readable:

    @{ $Arrays[$counter] } = split /\t/, $line;
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In scalar context (what you have), split returns the number of fields found (and older versions of Perl did split into the @_ array, issuing a "Use of implicit split to @_ is deprecated" warning).