[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556514 sequences (80000134 bp)...
[M::process] read 556524 sequences (80000138 bp)...
[M::mem_process_seqs] Processed 556514 reads in 148.460 CPU sec, 18.474 real sec
[M::process] read 556446 sequences (80000172 bp)...
[M::mem_process_seqs] Processed 556524 reads in 153.713 CPU sec, 18.859 real sec
[M::process] read 556450 sequences (80000142 bp)...
[M::mem_process_seqs] Processed 556446 reads in 153.334 CPU sec, 18.824 real sec
[M::process] read 83503 sequences (12004701 bp)...
[M::mem_process_seqs] Processed 556450 reads in 152.188 CPU sec, 18.788 real sec
[M::mem_process_seqs] Processed 83503 reads in 26.863 CPU sec, 3.168 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_FG137\tSM:CypressIslandWA_FG137\tPL:Illumina reference.fasta CypressIslandWA_FG137.R1.fq.gz
[main] Real time: 80.303 sec; CPU: 636.335 sec