[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000035 bp)...
[M::process] read 555560 sequences (80000239 bp)...
[M::mem_process_seqs] Processed 555558 reads in 165.787 CPU sec, 20.662 real sec
[M::process] read 555560 sequences (80000108 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.260 CPU sec, 20.796 real sec
[M::process] read 555560 sequences (80000222 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.757 CPU sec, 21.111 real sec
[M::process] read 555558 sequences (80000043 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.674 CPU sec, 20.974 real sec
[M::process] read 555558 sequences (80000023 bp)...
[M::mem_process_seqs] Processed 555558 reads in 168.002 CPU sec, 20.625 real sec
[M::process] read 555558 sequences (80000005 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.710 CPU sec, 20.832 real sec
[M::process] read 188028 sequences (27075917 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.188 CPU sec, 20.850 real sec
[M::mem_process_seqs] Processed 188028 reads in 60.194 CPU sec, 7.301 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:CypressIslandWA_FG106\tSM:CypressIslandWA_FG106\tPL:Illumina reference.fasta CypressIslandWA_FG106.R1.fq.gz
[main] Real time: 155.915 sec; CPU: 1246.582 sec