[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000069 bp)...
[M::process] read 555560 sequences (80000148 bp)...
[M::mem_process_seqs] Processed 555558 reads in 162.083 CPU sec, 20.217 real sec
[M::process] read 555560 sequences (80000278 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.695 CPU sec, 20.608 real sec
[M::process] read 555558 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.222 CPU sec, 20.435 real sec
[M::process] read 525270 sequences (75638577 bp)...
[M::mem_process_seqs] Processed 555558 reads in 163.738 CPU sec, 20.091 real sec
[M::mem_process_seqs] Processed 525270 reads in 153.421 CPU sec, 18.976 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_FG104-B\tSM:CypressIslandWA_FG104-B\tPL:Illumina reference.fasta CypressIslandWA_FG104-B.R1.fq.gz
[main] Real time: 104.771 sec; CPU: 816.058 sec