[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000269 bp)...
[M::process] read 555558 sequences (80000073 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.953 CPU sec, 20.294 real sec
[M::process] read 555560 sequences (80000249 bp)...
[M::mem_process_seqs] Processed 555558 reads in 171.166 CPU sec, 21.091 real sec
[M::process] read 555560 sequences (80000286 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.782 CPU sec, 20.979 real sec
[M::process] read 555558 sequences (80000038 bp)...
[M::mem_process_seqs] Processed 555560 reads in 168.363 CPU sec, 20.722 real sec
[M::process] read 555558 sequences (80000066 bp)...
[M::mem_process_seqs] Processed 555558 reads in 170.173 CPU sec, 20.874 real sec
[M::process] read 555558 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.571 CPU sec, 20.818 real sec
[M::process] read 28231 sequences (4065252 bp)...
[M::mem_process_seqs] Processed 555558 reads in 168.070 CPU sec, 20.793 real sec
[M::mem_process_seqs] Processed 28231 reads in 10.383 CPU sec, 1.221 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_FG101-B\tSM:CypressIslandWA_FG101-B\tPL:Illumina reference.fasta CypressIslandWA_FG101-B.R1.fq.gz
[main] Real time: 150.573 sec; CPU: 1193.858 sec