[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556346 sequences (80000210 bp)...
[M::process] read 556078 sequences (80000100 bp)...
[M::mem_process_seqs] Processed 556346 reads in 161.637 CPU sec, 20.157 real sec
[M::process] read 555938 sequences (80000215 bp)...
[M::mem_process_seqs] Processed 556078 reads in 169.272 CPU sec, 20.807 real sec
[M::process] read 556008 sequences (80000087 bp)...
[M::mem_process_seqs] Processed 555938 reads in 169.472 CPU sec, 20.796 real sec
[M::process] read 555990 sequences (80000217 bp)...
[M::mem_process_seqs] Processed 556008 reads in 167.897 CPU sec, 20.569 real sec
[M::process] read 555888 sequences (80000247 bp)...
[M::mem_process_seqs] Processed 555990 reads in 166.437 CPU sec, 20.452 real sec
[M::process] read 555890 sequences (80000059 bp)...
[M::mem_process_seqs] Processed 555888 reads in 169.774 CPU sec, 20.879 real sec
[M::process] read 154582 sequences (22248937 bp)...
[M::mem_process_seqs] Processed 555890 reads in 168.411 CPU sec, 20.784 real sec
[M::mem_process_seqs] Processed 154582 reads in 51.582 CPU sec, 6.212 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_FG184\tSM:PortGambleWA_FG184\tPL:Illumina reference.fasta PortGambleWA_FG184.R1.fq.gz
[main] Real time: 153.598 sec; CPU: 1226.378 sec