[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556122 sequences (80000133 bp)...
[M::process] read 556184 sequences (80000231 bp)...
[M::mem_process_seqs] Processed 556122 reads in 170.326 CPU sec, 21.225 real sec
[M::process] read 556106 sequences (80000259 bp)...
[M::mem_process_seqs] Processed 556184 reads in 175.073 CPU sec, 21.530 real sec
[M::process] read 406711 sequences (58500875 bp)...
[M::mem_process_seqs] Processed 556106 reads in 174.509 CPU sec, 21.484 real sec
[M::mem_process_seqs] Processed 406711 reads in 128.058 CPU sec, 15.796 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -L 20,5 -t 8 -a -M -T 10 -A 1 -B 4 -O 6 -R @RG\tID:MontereyBayCA_409\tSM:MontereyBayCA_409\tPL:Illumina reference.fasta MontereyBayCA_409.R1.fq.gz
[main] Real time: 84.834 sec; CPU: 650.848 sec