[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555884 sequences (80000090 bp)...
[M::process] read 555754 sequences (80000019 bp)...
[M::mem_process_seqs] Processed 555884 reads in 176.500 CPU sec, 22.027 real sec
[M::process] read 555748 sequences (80000129 bp)...
[M::mem_process_seqs] Processed 555754 reads in 179.799 CPU sec, 22.127 real sec
[M::process] read 555702 sequences (80000135 bp)...
[M::mem_process_seqs] Processed 555748 reads in 180.403 CPU sec, 22.173 real sec
[M::process] read 207479 sequences (29870029 bp)...
[M::mem_process_seqs] Processed 555702 reads in 178.616 CPU sec, 22.073 real sec
[M::mem_process_seqs] Processed 207479 reads in 71.747 CPU sec, 8.734 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_FG196\tSM:PortGambleWA_FG196\tPL:Illumina reference.fasta PortGambleWA_FG196.R1.fq.gz
[main] Real time: 100.245 sec; CPU: 789.199 sec