[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556264 sequences (80000063 bp)...
[M::process] read 556026 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 556264 reads in 168.100 CPU sec, 20.949 real sec
[M::process] read 555918 sequences (80000087 bp)...
[M::mem_process_seqs] Processed 556026 reads in 174.733 CPU sec, 21.511 real sec
[M::process] read 556024 sequences (80000184 bp)...
[M::mem_process_seqs] Processed 555918 reads in 176.405 CPU sec, 21.657 real sec
[M::process] read 555912 sequences (80000286 bp)...
[M::mem_process_seqs] Processed 556024 reads in 175.762 CPU sec, 21.634 real sec
[M::process] read 555880 sequences (80000084 bp)...
[M::mem_process_seqs] Processed 555912 reads in 178.473 CPU sec, 21.947 real sec
[M::process] read 121041 sequences (17422003 bp)...
[M::mem_process_seqs] Processed 555880 reads in 174.607 CPU sec, 21.576 real sec
[M::mem_process_seqs] Processed 121041 reads in 42.786 CPU sec, 5.120 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_FG195\tSM:PortGambleWA_FG195\tPL:Illumina reference.fasta PortGambleWA_FG195.R1.fq.gz
[main] Real time: 136.891 sec; CPU: 1092.567 sec