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       $id = getParent ($taxId);
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The variable $taxId is not available inside this subroutine so it's the same as saying:

       $id = getParent (undef);
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     while ($taxId = $taxId1){
        my $parent = `getz "[taxonomy:$taxId1]" -f pid`;
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The variable $taxId1 is not assigned a value until later in the subroutine and is not defined at all.