[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557110 sequences (80000036 bp)...
[M::process] read 557094 sequences (80000240 bp)...
[M::mem_process_seqs] Processed 557110 reads in 154.575 CPU sec, 19.206 real sec
[M::process] read 557132 sequences (80000072 bp)...
[M::mem_process_seqs] Processed 557094 reads in 157.874 CPU sec, 19.404 real sec
[M::process] read 557062 sequences (80000272 bp)...
[M::mem_process_seqs] Processed 557132 reads in 158.404 CPU sec, 19.421 real sec
[M::process] read 226294 sequences (32491512 bp)...
[M::mem_process_seqs] Processed 557062 reads in 155.677 CPU sec, 19.181 real sec
[M::mem_process_seqs] Processed 226294 reads in 66.253 CPU sec, 8.073 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_FG121\tSM:CypressIslandWA_FG121\tPL:Illumina reference.fasta CypressIslandWA_FG121.R1.fq.gz
[main] Real time: 88.499 sec; CPU: 695.039 sec