[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556090 sequences (80000068 bp)...
[M::process] read 556110 sequences (80000257 bp)...
[M::mem_process_seqs] Processed 556090 reads in 172.767 CPU sec, 21.537 real sec
[M::process] read 556070 sequences (80000157 bp)...
[M::mem_process_seqs] Processed 556110 reads in 175.810 CPU sec, 21.638 real sec
[M::process] read 11604 sequences (1668853 bp)...
[M::mem_process_seqs] Processed 556070 reads in 175.302 CPU sec, 21.681 real sec
[M::mem_process_seqs] Processed 11604 reads in 4.554 CPU sec, 0.534 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_439\tSM:MontereyBayCA_439\tPL:Illumina reference.fasta MontereyBayCA_439.R1.fq.gz
[main] Real time: 70.001 sec; CPU: 531.088 sec