[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556250 sequences (80000084 bp)...
[M::process] read 555996 sequences (80000272 bp)...
[M::mem_process_seqs] Processed 556250 reads in 160.308 CPU sec, 19.963 real sec
[M::process] read 555976 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 555996 reads in 169.641 CPU sec, 20.862 real sec
[M::process] read 396017 sequences (56991241 bp)...
[M::mem_process_seqs] Processed 555976 reads in 167.273 CPU sec, 20.625 real sec
[M::mem_process_seqs] Processed 396017 reads in 119.583 CPU sec, 14.725 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_FG198\tSM:PortGambleWA_FG198\tPL:Illumina reference.fasta PortGambleWA_FG198.R1.fq.gz
[main] Real time: 80.498 sec; CPU: 619.378 sec