[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000051 bp)...
[M::process] read 555560 sequences (80000286 bp)...
[M::mem_process_seqs] Processed 555558 reads in 164.771 CPU sec, 20.525 real sec
[M::process] read 555558 sequences (80000021 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.677 CPU sec, 20.480 real sec
[M::process] read 555560 sequences (80000274 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.588 CPU sec, 20.818 real sec
[M::process] read 555558 sequences (80000073 bp)...
[M::mem_process_seqs] Processed 555560 reads in 168.561 CPU sec, 20.701 real sec
[M::process] read 555558 sequences (80000076 bp)...
[M::mem_process_seqs] Processed 555558 reads in 167.031 CPU sec, 20.471 real sec
[M::process] read 449617 sequences (64744604 bp)...
[M::mem_process_seqs] Processed 555558 reads in 167.142 CPU sec, 20.562 real sec
[M::mem_process_seqs] Processed 449617 reads in 137.437 CPU sec, 16.971 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_FG109\tSM:CypressIslandWA_FG109\tPL:Illumina reference.fasta CypressIslandWA_FG109.R1.fq.gz
[main] Real time: 145.192 sec; CPU: 1144.193 sec