open ($ESTs_W_SNPs, '>', $output_file) or die "Cannot write to $o
+utput_file\n";
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Every time you open this file it will overwrite the previous contents of the file so that at the end of the loop only the last line will be saved.    Either move this open outside the loop so it only executes once, or open the file in append mode so that the file doesn't get overwritten.