[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556118 sequences (80000246 bp)...
[M::process] read 556170 sequences (80000226 bp)...
[M::mem_process_seqs] Processed 556118 reads in 154.257 CPU sec, 19.194 real sec
[M::process] read 556118 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 556170 reads in 160.421 CPU sec, 19.710 real sec
[M::process] read 208215 sequences (29947160 bp)...
[M::mem_process_seqs] Processed 556118 reads in 160.801 CPU sec, 19.865 real sec
[M::mem_process_seqs] Processed 208215 reads in 62.370 CPU sec, 7.569 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_440\tSM:MontereyBayCA_440\tPL:Illumina reference.fasta MontereyBayCA_440.R1.fq.gz
[main] Real time: 69.092 sec; CPU: 539.847 sec