[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556598 sequences (80000061 bp)...
[M::process] read 556612 sequences (80000229 bp)...
[M::mem_process_seqs] Processed 556598 reads in 147.435 CPU sec, 18.348 real sec
[M::process] read 556588 sequences (80000213 bp)...
[M::mem_process_seqs] Processed 556612 reads in 151.531 CPU sec, 18.620 real sec
[M::process] read 556580 sequences (80000250 bp)...
[M::mem_process_seqs] Processed 556588 reads in 151.068 CPU sec, 18.483 real sec
[M::process] read 111910 sequences (16083000 bp)...
[M::mem_process_seqs] Processed 556580 reads in 148.166 CPU sec, 18.276 real sec
[M::mem_process_seqs] Processed 111910 reads in 33.925 CPU sec, 4.012 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:CypressIslandWA_FG114\tSM:CypressIslandWA_FG114\tPL:Illumina reference.fasta CypressIslandWA_FG114.R1.fq.gz
[main] Real time: 80.123 sec; CPU: 633.910 sec