[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557072 sequences (80000089 bp)...
[M::process] read 557060 sequences (80000239 bp)...
[M::mem_process_seqs] Processed 557072 reads in 147.800 CPU sec, 18.402 real sec
[M::process] read 557116 sequences (80000104 bp)...
[M::mem_process_seqs] Processed 557060 reads in 153.892 CPU sec, 18.901 real sec
[M::process] read 557046 sequences (80000278 bp)...
[M::mem_process_seqs] Processed 557116 reads in 152.591 CPU sec, 18.742 real sec
[M::process] read 512965 sequences (73661312 bp)...
[M::mem_process_seqs] Processed 557046 reads in 153.236 CPU sec, 18.817 real sec
[M::mem_process_seqs] Processed 512965 reads in 136.788 CPU sec, 16.909 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_FG129\tSM:CypressIslandWA_FG129\tPL:Illumina reference.fasta CypressIslandWA_FG129.R1.fq.gz
[main] Real time: 96.322 sec; CPU: 747.099 sec