bwa -mem log messages

Question

[aleka]

Hello,

I am using bwa mem to aligh paired ends and I get the following errors:

[M::process] read 1057202 sequences (80000122 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 440646, 0, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (100, 120, 148)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (4, 244)
[M::mem_pestat] mean and std.dev: (125.80, 35.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 292)
[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 1056888 reads in 132.524 CPU sec, 132.576 real sec

Please let me know if you have any idea of what this might be.

Best.

Answer 1

[Istvan Albert]

None of these are error messages.

Different library preparations and sequencing instruments may read DNA fragments in different orientations.

bwa tries all these orientations to detect your fragment sizes.

So these messages just say that all your reads seem to be in FR orientation - which is the most common library prep.