[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555820 sequences (80000260 bp)...
[M::process] read 555874 sequences (80000154 bp)...
[M::mem_process_seqs] Processed 555820 reads in 170.310 CPU sec, 21.223 real sec
[M::process] read 555766 sequences (80000108 bp)...
[M::mem_process_seqs] Processed 555874 reads in 174.824 CPU sec, 21.468 real sec
[M::process] read 555756 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 555766 reads in 177.302 CPU sec, 21.754 real sec
[M::process] read 149497 sequences (21517256 bp)...
[M::mem_process_seqs] Processed 555756 reads in 177.261 CPU sec, 21.878 real sec
[M::mem_process_seqs] Processed 149497 reads in 51.291 CPU sec, 6.190 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_417\tSM:MontereyBayCA_417\tPL:Illumina reference.fasta MontereyBayCA_417.R1.fq.gz
[main] Real time: 95.122 sec; CPU: 752.776 sec