[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556102 sequences (80000102 bp)...
[M::process] read 555870 sequences (80000248 bp)...
[M::mem_process_seqs] Processed 556102 reads in 160.675 CPU sec, 19.992 real sec
[M::process] read 555786 sequences (80000212 bp)...
[M::mem_process_seqs] Processed 555870 reads in 169.569 CPU sec, 20.871 real sec
[M::process] read 555780 sequences (80000221 bp)...
[M::mem_process_seqs] Processed 555786 reads in 171.323 CPU sec, 21.018 real sec
[M::process] read 555736 sequences (80000040 bp)...
[M::mem_process_seqs] Processed 555780 reads in 170.050 CPU sec, 20.909 real sec
[M::process] read 511213 sequences (73592621 bp)...
[M::mem_process_seqs] Processed 555736 reads in 171.682 CPU sec, 21.101 real sec
[M::mem_process_seqs] Processed 511213 reads in 156.294 CPU sec, 19.328 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_FG183\tSM:PortGambleWA_FG183\tPL:Illumina reference.fasta PortGambleWA_FG183.R1.fq.gz
[main] Real time: 128.780 sec; CPU: 1002.646 sec