[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556230 sequences (80000183 bp)...
[M::process] read 555966 sequences (80000261 bp)...
[M::mem_process_seqs] Processed 556230 reads in 164.394 CPU sec, 20.509 real sec
[M::process] read 555960 sequences (80000153 bp)...
[M::mem_process_seqs] Processed 555966 reads in 166.760 CPU sec, 20.520 real sec
[M::process] read 555946 sequences (80000286 bp)...
[M::mem_process_seqs] Processed 555960 reads in 168.842 CPU sec, 20.758 real sec
[M::process] read 555840 sequences (80000063 bp)...
[M::mem_process_seqs] Processed 555946 reads in 168.634 CPU sec, 20.711 real sec
[M::process] read 274244 sequences (39472034 bp)...
[M::mem_process_seqs] Processed 555840 reads in 167.960 CPU sec, 20.718 real sec
[M::mem_process_seqs] Processed 274244 reads in 85.583 CPU sec, 10.469 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_FG197\tSM:PortGambleWA_FG197\tPL:Illumina reference.fasta PortGambleWA_FG197.R1.fq.gz
[main] Real time: 117.082 sec; CPU: 924.431 sec