[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555836 sequences (80000287 bp)...
[M::process] read 555732 sequences (80000009 bp)...
[M::mem_process_seqs] Processed 555836 reads in 164.567 CPU sec, 20.512 real sec
[M::process] read 555714 sequences (80000111 bp)...
[M::mem_process_seqs] Processed 555732 reads in 174.593 CPU sec, 21.494 real sec
[M::process] read 555676 sequences (80000075 bp)...
[M::mem_process_seqs] Processed 555714 reads in 175.697 CPU sec, 21.560 real sec
[M::process] read 220584 sequences (31758125 bp)...
[M::mem_process_seqs] Processed 555676 reads in 171.396 CPU sec, 21.154 real sec
[M::mem_process_seqs] Processed 220584 reads in 73.011 CPU sec, 8.911 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_FG194\tSM:PortGambleWA_FG194\tPL:Illumina reference.fasta PortGambleWA_FG194.R1.fq.gz
[main] Real time: 96.608 sec; CPU: 761.261 sec