Known IssuesΒΆ

  • 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 ‘’, 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)

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