I'm a relative newbie and trying t work my way through using bwa mem. I've successfully aligned PE reads to a reference genome previously using bwa aln but I thought this might work better.
I'm getting the following output:
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2012726 reads in 2859.953 CPU sec, 143.173 real sec
I could be wrong but I think this may be a problem with my index. I'm attempting to use the same indexed reference genome as my bwa aln work. The bwa manual suggests that there is a different algorithm for building the index for use with bwa mem. Is that true? If so, I can't figure out how to implement it.
Any help would be appreciated.