[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557246 sequences (80000192 bp)...
[M::process] read 557222 sequences (80000201 bp)...
[M::mem_process_seqs] Processed 557246 reads in 147.117 CPU sec, 18.320 real sec
[M::process] read 557284 sequences (80000249 bp)...
[M::mem_process_seqs] Processed 557222 reads in 151.514 CPU sec, 18.599 real sec
[M::process] read 557158 sequences (80000215 bp)...
[M::mem_process_seqs] Processed 557284 reads in 150.792 CPU sec, 18.513 real sec
[M::process] read 349745 sequences (50202898 bp)...
[M::mem_process_seqs] Processed 557158 reads in 149.203 CPU sec, 18.358 real sec
[M::mem_process_seqs] Processed 349745 reads in 95.408 CPU sec, 11.736 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_FG145\tSM:CypressIslandWA_FG145\tPL:Illumina reference.fasta CypressIslandWA_FG145.R1.fq.gz
[main] Real time: 89.764 sec; CPU: 696.685 sec