[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556298 sequences (80000110 bp)...
[M::process] read 556374 sequences (80000078 bp)...
[M::mem_process_seqs] Processed 556298 reads in 159.252 CPU sec, 19.847 real sec
[M::process] read 556266 sequences (80000221 bp)...
[M::mem_process_seqs] Processed 556374 reads in 165.408 CPU sec, 20.316 real sec
[M::process] read 556296 sequences (80000131 bp)...
[M::mem_process_seqs] Processed 556266 reads in 166.587 CPU sec, 20.470 real sec
[M::process] read 109958 sequences (15810016 bp)...
[M::mem_process_seqs] Processed 556296 reads in 163.742 CPU sec, 20.222 real sec
[M::mem_process_seqs] Processed 109958 reads in 36.798 CPU sec, 4.371 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_FG133\tSM:CypressIslandWA_FG133\tPL:Illumina reference.fasta CypressIslandWA_FG133.R1.fq.gz
[main] Real time: 87.209 sec; CPU: 693.325 sec