[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556820 sequences (80000233 bp)...
[M::process] read 556902 sequences (80000150 bp)...
[M::mem_process_seqs] Processed 556820 reads in 154.670 CPU sec, 19.249 real sec
[M::process] read 556870 sequences (80000078 bp)...
[M::mem_process_seqs] Processed 556902 reads in 158.848 CPU sec, 19.489 real sec
[M::process] read 556836 sequences (80000091 bp)...
[M::mem_process_seqs] Processed 556870 reads in 159.232 CPU sec, 19.504 real sec
[M::process] read 556788 sequences (80000036 bp)...
[M::mem_process_seqs] Processed 556836 reads in 159.514 CPU sec, 19.572 real sec
[M::process] read 390140 sequences (56044997 bp)...
[M::mem_process_seqs] Processed 556788 reads in 158.314 CPU sec, 19.479 real sec
[M::mem_process_seqs] Processed 390140 reads in 111.880 CPU sec, 13.771 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_FG181\tSM:PortGambleWA_FG181\tPL:Illumina reference.fasta PortGambleWA_FG181.R1.fq.gz
[main] Real time: 115.086 sec; CPU: 905.172 sec