[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556684 sequences (80000123 bp)...
[M::process] read 556700 sequences (80000153 bp)...
[M::mem_process_seqs] Processed 556684 reads in 155.713 CPU sec, 19.390 real sec
[M::process] read 556688 sequences (80000286 bp)...
[M::mem_process_seqs] Processed 556700 reads in 157.553 CPU sec, 19.371 real sec
[M::process] read 556686 sequences (80000111 bp)...
[M::mem_process_seqs] Processed 556688 reads in 158.765 CPU sec, 19.494 real sec
[M::process] read 556656 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 556686 reads in 160.648 CPU sec, 19.725 real sec
[M::process] read 173140 sequences (24879160 bp)...
[M::mem_process_seqs] Processed 556656 reads in 161.011 CPU sec, 19.853 real sec
[M::mem_process_seqs] Processed 173140 reads in 53.524 CPU sec, 6.472 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_Q418\tSM:MontereyBayCA_Q418\tPL:Illumina reference.fasta MontereyBayCA_Q418.R1.fq.gz
[main] Real time: 107.093 sec; CPU: 849.072 sec