[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555842 sequences (80000231 bp)...
[M::process] read 555834 sequences (80000010 bp)...
[M::mem_process_seqs] Processed 555842 reads in 177.917 CPU sec, 22.192 real sec
[M::process] read 555744 sequences (80000001 bp)...
[M::mem_process_seqs] Processed 555834 reads in 180.739 CPU sec, 22.236 real sec
[M::process] read 172218 sequences (24787904 bp)...
[M::mem_process_seqs] Processed 555744 reads in 179.367 CPU sec, 22.149 real sec
[M::mem_process_seqs] Processed 172218 reads in 59.943 CPU sec, 7.260 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_405\tSM:MontereyBayCA_405\tPL:Illumina reference.fasta MontereyBayCA_405.R1.fq.gz
[main] Real time: 76.773 sec; CPU: 600.161 sec