[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556058 sequences (80000079 bp)...
[M::process] read 555874 sequences (80000082 bp)...
[M::mem_process_seqs] Processed 556058 reads in 162.107 CPU sec, 20.204 real sec
[M::process] read 555774 sequences (80000274 bp)...
[M::mem_process_seqs] Processed 555874 reads in 170.419 CPU sec, 20.944 real sec
[M::process] read 555756 sequences (80000202 bp)...
[M::mem_process_seqs] Processed 555774 reads in 172.074 CPU sec, 21.133 real sec
[M::process] read 555728 sequences (80000024 bp)...
[M::mem_process_seqs] Processed 555756 reads in 171.447 CPU sec, 21.020 real sec
[M::process] read 555712 sequences (80000129 bp)...
[M::mem_process_seqs] Processed 555728 reads in 172.032 CPU sec, 21.125 real sec
[M::process] read 261985 sequences (37716874 bp)...
[M::mem_process_seqs] Processed 555712 reads in 167.017 CPU sec, 20.567 real sec
[M::mem_process_seqs] Processed 261985 reads in 82.621 CPU sec, 10.097 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_FG186\tSM:PortGambleWA_FG186\tPL:Illumina reference.fasta PortGambleWA_FG186.R1.fq.gz
[main] Real time: 138.681 sec; CPU: 1100.184 sec