[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556698 sequences (80000013 bp)...
[M::process] read 556688 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 556698 reads in 149.337 CPU sec, 18.584 real sec
[M::process] read 556704 sequences (80000129 bp)...
[M::mem_process_seqs] Processed 556688 reads in 152.993 CPU sec, 18.800 real sec
[M::process] read 556652 sequences (80000259 bp)...
[M::mem_process_seqs] Processed 556704 reads in 153.364 CPU sec, 18.810 real sec
[M::process] read 403598 sequences (57992038 bp)...
[M::mem_process_seqs] Processed 556652 reads in 153.192 CPU sec, 18.826 real sec
[M::mem_process_seqs] Processed 403598 reads in 111.645 CPU sec, 13.751 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_FG189\tSM:PortGambleWA_FG189\tPL:Illumina reference.fasta PortGambleWA_FG189.R1.fq.gz
[main] Real time: 92.663 sec; CPU: 723.030 sec