I've been trying to use the 'Du Novo' sequencing pipeline to analyze a set of bacterial whole genome sequencing data. This is the paper outlining the method: Streamlined analysis of duplex sequencing data with Du Novo. At the 9th step, the pipeline suggests using a function from the package 'freebayes' called 'bamleftalign'. I've tried using this function as I've listed below.
bamleftalign duplex.filt.aln.sort.bam -f ref.fasta > output.bam
For some reason, it doesn't provide an output -- it leaves the output.bam file empty. Is there something wrong with my usage of the function?
Is there something else that I should be checking? I checked the function in my PATH and I've ran and passed the freebayes package test files.
Any and all input would be appreciated!