[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556958 sequences (80000172 bp)...
[M::process] read 556950 sequences (80000224 bp)...
[M::mem_process_seqs] Processed 556958 reads in 143.622 CPU sec, 17.875 real sec
[M::process] read 556966 sequences (80000183 bp)...
[M::mem_process_seqs] Processed 556950 reads in 146.687 CPU sec, 17.990 real sec
[M::process] read 556930 sequences (80000140 bp)...
[M::mem_process_seqs] Processed 556966 reads in 146.127 CPU sec, 17.913 real sec
[M::process] read 215491 sequences (30950951 bp)...
[M::mem_process_seqs] Processed 556930 reads in 146.196 CPU sec, 18.024 real sec
[M::mem_process_seqs] Processed 215491 reads in 60.695 CPU sec, 7.396 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_FG116\tSM:CypressIslandWA_FG116\tPL:Illumina reference.fasta CypressIslandWA_FG116.R1.fq.gz
[main] Real time: 82.496 sec; CPU: 645.710 sec