[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556284 sequences (80000136 bp)...
[M::process] read 555970 sequences (80000283 bp)...
[M::mem_process_seqs] Processed 556284 reads in 161.486 CPU sec, 20.126 real sec
[M::process] read 556006 sequences (80000182 bp)...
[M::mem_process_seqs] Processed 555970 reads in 171.957 CPU sec, 21.128 real sec
[M::process] read 555938 sequences (80000272 bp)...
[M::mem_process_seqs] Processed 556006 reads in 169.230 CPU sec, 20.780 real sec
[M::process] read 555862 sequences (80000054 bp)...
[M::mem_process_seqs] Processed 555938 reads in 170.887 CPU sec, 20.974 real sec
[M::process] read 72660 sequences (10458392 bp)...
[M::mem_process_seqs] Processed 555862 reads in 166.653 CPU sec, 20.585 real sec
[M::mem_process_seqs] Processed 72660 reads in 26.248 CPU sec, 3.128 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_FG185\tSM:PortGambleWA_FG185\tPL:Illumina reference.fasta PortGambleWA_FG185.R1.fq.gz
[main] Real time: 110.161 sec; CPU: 868.772 sec