[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556390 sequences (80000028 bp)...
[M::process] read 556386 sequences (80000088 bp)...
[M::mem_process_seqs] Processed 556390 reads in 147.149 CPU sec, 18.314 real sec
[M::process] read 556396 sequences (80000200 bp)...
[M::mem_process_seqs] Processed 556386 reads in 153.489 CPU sec, 18.813 real sec
[M::process] read 556370 sequences (80000145 bp)...
[M::mem_process_seqs] Processed 556396 reads in 153.672 CPU sec, 18.820 real sec
[M::process] read 556388 sequences (80000071 bp)...
[M::mem_process_seqs] Processed 556370 reads in 152.379 CPU sec, 18.669 real sec
[M::process] read 17298 sequences (2486384 bp)...
[M::mem_process_seqs] Processed 556388 reads in 151.142 CPU sec, 18.665 real sec
[M::mem_process_seqs] Processed 17298 reads in 5.748 CPU sec, 0.684 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_FG126\tSM:CypressIslandWA_FG126\tPL:Illumina reference.fasta CypressIslandWA_FG126.R1.fq.gz
[main] Real time: 98.790 sec; CPU: 766.716 sec