[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 539504 sequences (80116344 bp)...
[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 539504 reads in 32.157 CPU sec, 2.173 real sec
[main] Version: 0.7.15-r1142-dirty
[main] CMD: bwa mem -L 20,5 -t 40 -a -M -T 10 -A 1 -B 3 -O 5 -R @RG\tID:313_Coleman-Connectivity_P1P4\tSM:313_Coleman-Connectivity_P1P4\tPL:Illumina reference.174.174.fasta 313_Coleman-Connectivity_P1P4.R1.fq.gz 313_Coleman-Connectivity_P1P4.R2.fq.gz
[main] Real time: 7.784 sec; CPU: 34.612 sec