[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557136 sequences (80000145 bp)...
[M::process] read 557110 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 557136 reads in 149.494 CPU sec, 18.611 real sec
[M::process] read 557142 sequences (80000271 bp)...
[M::mem_process_seqs] Processed 557110 reads in 152.840 CPU sec, 18.789 real sec
[M::process] read 557052 sequences (80000035 bp)...
[M::mem_process_seqs] Processed 557142 reads in 154.165 CPU sec, 18.904 real sec
[M::process] read 361064 sequences (51837781 bp)...
[M::mem_process_seqs] Processed 557052 reads in 151.378 CPU sec, 18.598 real sec
[M::mem_process_seqs] Processed 361064 reads in 101.057 CPU sec, 12.425 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_FG124\tSM:CypressIslandWA_FG124\tPL:Illumina reference.fasta CypressIslandWA_FG124.R1.fq.gz
[main] Real time: 91.190 sec; CPU: 711.468 sec