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lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) #378

Open crispychilli opened 2 years ago

crispychilli commented 2 years ago

I would like to take a mapping with bwa_mem on a reference consisting of 160bp sequences, but I got the following report:

[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 2199456 reads in 1296.217 CPU sec, 33.289 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -t 40 lunyu M3_pe150_L2_1.fq.gz M3_pe150_L2_1.fq.gz [main] Real time: 1098.701 sec; CPU: 42385.799 sec [bam_sort_core] merging from 0 files and 40 in-memory blocks...

Sequencing data are PE150 reads produced by illumina platform. Is there a minimum size for the reference with bwa index? When the reference is a short sequence, how to get the correct mapping result?

Thanks for your help. Leslie