Known Issues
============
* cdbfasta cannot handle very large databases. A possible work-around is to 
  split the source FASTA database files into two or more files of suitable size 
  for cdbfasta.

* The pipeline does not prompt when overwriting output files so there is a risk 
  of overwriting results if user is not careful.

* If the user wishes to retrieve full-length sequences from the databases, 
  BLASTclust might have a hard time clustering the results (i.e. it will 
  probably crash) if at least one of the sequences are complete genomes.

* The pipeline currently is intended to search for Qnr-like genes and assumes 
  that the five known plasmid mediated Qnr-genes are the ones to align each 
  cluster against (the experimental -R option). This can be modified if the user 
  desires by a modification in the source code in 'fluff.py', function 
  fluff.malign_clusters() around line 1029 (and making sure that the names stated 
  on this line is in the sequence identifiers in the file at CLUSTSEQPATH)