[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557082 sequences (80000244 bp)...
[M::process] read 557060 sequences (80000252 bp)...
[M::mem_process_seqs] Processed 557082 reads in 150.852 CPU sec, 18.764 real sec
[M::process] read 557074 sequences (80000234 bp)...
[M::mem_process_seqs] Processed 557060 reads in 155.602 CPU sec, 19.120 real sec
[M::process] read 557002 sequences (80000157 bp)...
[M::mem_process_seqs] Processed 557074 reads in 155.350 CPU sec, 19.027 real sec
[M::process] read 280923 sequences (40341487 bp)...
[M::mem_process_seqs] Processed 557002 reads in 152.327 CPU sec, 18.746 real sec
[M::mem_process_seqs] Processed 280923 reads in 79.716 CPU sec, 9.756 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_FG122\tSM:CypressIslandWA_FG122\tPL:Illumina reference.fasta CypressIslandWA_FG122.R1.fq.gz
[main] Real time: 88.594 sec; CPU: 695.875 sec