[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555926 sequences (80000081 bp)...
[M::process] read 555780 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 555926 reads in 155.663 CPU sec, 19.404 real sec
[M::process] read 555786 sequences (80000115 bp)...
[M::mem_process_seqs] Processed 555780 reads in 161.094 CPU sec, 19.780 real sec
[M::process] read 555734 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 555786 reads in 159.041 CPU sec, 19.543 real sec
[M::process] read 309135 sequences (44502371 bp)...
[M::mem_process_seqs] Processed 555734 reads in 161.931 CPU sec, 19.919 real sec
[M::mem_process_seqs] Processed 309135 reads in 92.005 CPU sec, 11.301 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_FG190\tSM:PortGambleWA_FG190\tPL:Illumina reference.fasta PortGambleWA_FG190.R1.fq.gz
[main] Real time: 93.710 sec; CPU: 732.315 sec