[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555856 sequences (80000030 bp)...
[M::process] read 555752 sequences (80000209 bp)...
[M::mem_process_seqs] Processed 555856 reads in 167.004 CPU sec, 20.840 real sec
[M::process] read 555734 sequences (80000075 bp)...
[M::mem_process_seqs] Processed 555752 reads in 173.432 CPU sec, 21.356 real sec
[M::process] read 555706 sequences (80000021 bp)...
[M::mem_process_seqs] Processed 555734 reads in 169.789 CPU sec, 20.804 real sec
[M::process] read 555674 sequences (80000171 bp)...
[M::mem_process_seqs] Processed 555706 reads in 174.792 CPU sec, 21.442 real sec
[M::process] read 204298 sequences (29413407 bp)...
[M::mem_process_seqs] Processed 555674 reads in 172.025 CPU sec, 21.242 real sec
[M::mem_process_seqs] Processed 204298 reads in 66.373 CPU sec, 8.078 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:PortGambleWA_FG182\tSM:PortGambleWA_FG182\tPL:Illumina reference.fasta PortGambleWA_FG182.R1.fq.gz
[main] Real time: 116.652 sec; CPU: 925.432 sec