[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555884 sequences (80000058 bp)...
[M::process] read 555886 sequences (80000016 bp)...
[M::mem_process_seqs] Processed 555884 reads in 177.364 CPU sec, 22.072 real sec
[M::process] read 555826 sequences (80000233 bp)...
[M::mem_process_seqs] Processed 555886 reads in 181.905 CPU sec, 22.365 real sec
[M::process] read 82356 sequences (11852058 bp)...
[M::mem_process_seqs] Processed 555826 reads in 181.239 CPU sec, 22.421 real sec
[M::mem_process_seqs] Processed 82356 reads in 31.250 CPU sec, 3.686 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_422\tSM:MontereyBayCA_422\tPL:Illumina reference.fasta MontereyBayCA_422.R1.fq.gz
[main] Real time: 73.038 sec; CPU: 573.579 sec