The error is on line 69

while($line=<TRF>)
    {
#          @line=split("\t",$trftable); # error 
          @line=split("\t",$line);
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also you probably want the merge file in the same folder as the other 2 files

open MERGE,">","$folder/merge" 
        or die "Could not open $folder/merge : $!";
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poj