[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556094 sequences (80000050 bp)...
[M::process] read 555892 sequences (80000048 bp)...
[M::mem_process_seqs] Processed 556094 reads in 159.075 CPU sec, 19.808 real sec
[M::process] read 555796 sequences (80000123 bp)...
[M::mem_process_seqs] Processed 555892 reads in 166.778 CPU sec, 20.495 real sec
[M::process] read 555754 sequences (80000133 bp)...
[M::mem_process_seqs] Processed 555796 reads in 170.871 CPU sec, 20.971 real sec
[M::process] read 555746 sequences (80000186 bp)...
[M::mem_process_seqs] Processed 555754 reads in 166.521 CPU sec, 20.431 real sec
[M::process] read 555714 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 555746 reads in 167.901 CPU sec, 20.640 real sec
[M::process] read 555708 sequences (80000246 bp)...
[M::mem_process_seqs] Processed 555714 reads in 168.244 CPU sec, 20.627 real sec
[M::process] read 11558 sequences (1663983 bp)...
[M::mem_process_seqs] Processed 555708 reads in 167.495 CPU sec, 20.709 real sec
[M::mem_process_seqs] Processed 11558 reads in 4.357 CPU sec, 0.535 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_FG187\tSM:PortGambleWA_FG187\tPL:Illumina reference.fasta PortGambleWA_FG187.R1.fq.gz
[main] Real time: 149.552 sec; CPU: 1174.548 sec