[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556202 sequences (80000180 bp)...
[M::process] read 555918 sequences (80000246 bp)...
[M::mem_process_seqs] Processed 556202 reads in 161.383 CPU sec, 20.116 real sec
[M::process] read 555974 sequences (80000197 bp)...
[M::mem_process_seqs] Processed 555918 reads in 168.693 CPU sec, 20.742 real sec
[M::process] read 555852 sequences (80000138 bp)...
[M::mem_process_seqs] Processed 555974 reads in 167.575 CPU sec, 20.561 real sec
[M::process] read 152416 sequences (21937758 bp)...
[M::mem_process_seqs] Processed 555852 reads in 167.611 CPU sec, 20.687 real sec
[M::mem_process_seqs] Processed 152416 reads in 50.823 CPU sec, 6.138 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_FG192\tSM:PortGambleWA_FG192\tPL:Illumina reference.fasta PortGambleWA_FG192.R1.fq.gz
[main] Real time: 91.118 sec; CPU: 718.039 sec