README update

README.md

@@ -114,7 +114,19 @@ This corresponds to the protein `00141` of the element `ESCO001.0321.00001.P001`
 **WARNING**: if your run is not properly configured, you can completely exhaust your system.
 
 ## Output
-wGRR produces a table with the following columns:
+Provided `wGRR` was executed with the `-o OUT` option, it will create several files.
+
+1. OUT.allpairs.txt contains all pairs of genetic elements, one per line.
+
+2. OUT.m8 is the output of `MMseqs` and contain all the significant protein-protein comparisons.
+
+3. OUT.mmseqs.search.log is the log file of the `MMseqs` step.
+
+4. OUT.bbh.txt contains all the identified BBH. The columns are 'query target identity query_coverage,target_coverage'
+
+5. OUT.wgrr.log is the log file of `wGRR`
+
+6. OUT.wgrr.txt is the final wGRR table. It contains the following columns:
 
 The first two columns indicate the pair of elements for this row.