[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556644 sequences (80000077 bp)...
[M::process] read 556644 sequences (80000205 bp)...
[M::mem_process_seqs] Processed 556644 reads in 150.836 CPU sec, 18.772 real sec
[M::process] read 556656 sequences (80000204 bp)...
[M::mem_process_seqs] Processed 556644 reads in 153.948 CPU sec, 18.902 real sec
[M::process] read 556636 sequences (80000145 bp)...
[M::mem_process_seqs] Processed 556656 reads in 153.910 CPU sec, 18.840 real sec
[M::process] read 533811 sequences (76715714 bp)...
[M::mem_process_seqs] Processed 556636 reads in 156.857 CPU sec, 19.275 real sec
[M::mem_process_seqs] Processed 533811 reads in 149.618 CPU sec, 18.489 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_FG138\tSM:CypressIslandWA_FG138\tPL:Illumina reference.fasta CypressIslandWA_FG138.R1.fq.gz
[main] Real time: 99.019 sec; CPU: 768.109 sec