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)